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2013 Scientific Report

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VARI | 2013 Research Interests Hormone signaling is essential to eukaryotic life. Our research is focused on the signaling mechanisms of physiologically important hormones, striving to solve fundamental questions that have a broad impact on human health and disease. The overall goal of my research program is to seek new biological paradigms through structural and functional analysis of key hormone signaling complexes and to develop therapeutic applications using the structural information we obtain. My current research programs are focused on two families of proteins, the nuclear hormone receptors and the G protein–coupled receptors, because these proteins, beyond their fundamental roles in biology, are important drug targets for treating major human diseases. Nuclear hormone receptors Nuclear hormone receptors are a large family comprising ligand-regulated and DNA-binding transcriptional factors, which include receptors for classic steroid hormones such as estrogen, progesterone, androgens, and glucocorticoids, as well as receptors for peroxisome proliferator activators, vitamin D, vitamin A, and thyroid hormones. One distinguishing fact about these classic receptors is that they are among the most successful targets in the history of drug discovery. Every receptor has one or more cognate synthetic ligands being used as medicines. Nuclear receptors also include a class of “orphan” receptors for which no ligand has been identified. In the last five years, we have developed the following projects centering on the structural biology of nuclear receptors. Peroxisome proliferator–activated receptors The peroxisome proliferator–activated receptors (PPAR a, d, and g) are the key regulators of glucose and fatty acid homeostasis and as such are important therapeutic targets for treating cardiovascular disease, diabetes, and cancer. Millions of patients have benefited from treatment with the novel PPARg ligands rosiglitazone and pioglitazone for type II diabetes. To understand the molecular basis of ligand-mediated signaling by PPARs, we have determined crystal structures of each PPAR’s ligandbinding domain (LBD) bound to many diverse ligands, including fatty acids, the lipid-lowering drugs called fibrates, and the new generation of anti-diabetic drugs, the glitazones. We have also determined the crystal structures of these receptors bound to co-activators or co-repressors, and the crystal structure of PPARg bound to a nitrated fatty acid. These structures have provided a framework for understanding the mechanisms of agonists and antagonists, as well as the recruitment of co-activators and co-repressors in gene activation and repression. Furthermore, these structures serve as a molecular basis for understanding the potency, selectivity, and binding mode of diverse ligands, and have provided crucial insights for designing the next generation of PPAR medicines. We have discovered a number of natural ligands of PPARg, and our plan is to test their physiological roles in glucose and insulin regulation, to unravel their molecular and structural mechanisms of action, and to develop them into therapeutics for diabetes and dislipidemia. The human glucocorticoid receptor The human glucocorticoid receptor (GR), the prototype steroid hormone receptor, is crucial for a wide spectrum of human physiology including immune/inflammatory responses, metabolic homeostasis, and control of blood pressure. GR is a wellestablished target for drugs, and those drugs have an annual market of over billion. GR ligands such as dexamethasone (Dex) and fluticasone propionate (FP) are used to treat asthma, leukemia, and autoimmune diseases. However, the clinical use of these ligands is limited by undesirable side effects partly associated with their receptor cross-reactivity or low potency. The discovery of potent and more-selective GR ligands—called “dissociated glucocorticoids”, which can separate the good effects from the bad—remains an intensive goal of pharmaceutical research. We have determined a number of crystal structures of GR bound to unique ligands and have found an unexpected regulatory mechanism: GR degradation by lysosomes. We also are studying the molecular and structural mechanisms of the dissociated glucocorticoids identified by our research. 71

Van Andel Research Institute | Scientific Report Structural genomics of nuclear receptor ligand-binding domains The LBD of a nuclear receptor contains key structural elements that mediate ligand-dependent regulation of the receptors and as such has been the focus of intense structural studies. Crystal structures for more than half of the 48 human nuclear receptors have been determined. These structures have illustrated the details of ligand binding, the conformational changes induced by agonists and antagonists, the basis of dimerization, and the mechanism of co-activator and co-repressor binding. The structures also have provided many surprises regarding the identity of ligands, the size and shape of the ligand-binding pockets, and the structural implications of the receptor signaling pathways. There are only a few orphan nuclear receptors for which the LBD structure remains unsolved; in the past few years, we have determined the crystal structures of those for CAR, SHP, SF-1, COUP-TFII, and LRH-1. Our structures have helped to identify new ligands and signaling mechanisms for orphan nuclear receptors. G protein–coupled receptors (GPCRs) The GPCRs form the largest family of receptors in the human genome. They receive a diverse set of signals carried by photons, ions, small chemicals, peptides, and large protein hormones. These receptors account for over 40% of drug targets, but their structures remain a challenge, because they are seven-transmembrane receptors. There are only a few crystal structures for class A GPCRs, and many important questions regarding GPCR ligand binding and activation remain unanswered. From our standpoint, GPCRs are similar to nuclear hormone receptors with respect to regulation by protein-ligand and proteinprotein interactions. Currently my group is focused on class B GPCRs, which includes receptors for parathyroid hormone (PTH), corticotropin-releasing factor (CRF), glucagon, and glucagon-like peptide-1. We have determined crystal structures of the ligand binding domain of the PTH receptor and the CRF receptor, and we are developing hormone analogs for treating osteoporosis, depression, and diabetes. In addition, we are developing a mammalian overexpression system and plan to use it to express full-length GPCRs for crystallization and structural studies. Recent Publications Ke, Jiyuan, Chenghai Zhang, Kaleeckal G. Harikumar, Cassandra R. Zylstra-Diegel, Liren Wang, Laura E. Mowry, Laurence J. Miller, Bart O. Williams, and H. Eric Xu. 2012. Modulation of b-catenin signaling by glucagon receptor activation. PLoS One 7(3): e33676. Pal, Kuntal, Karsten Melcher, and H. Eric Xu. 2012. Structure and mechanism for recognition of peptide hormones by Class B G-protein-coupled receptors. Acta Pharmacologica Sinica 33(3): 300–311. Soon, Fen-Fen, Ley-Moy Ng, X. Edward Zhou, Graham M. West, Amanda Kovach, M.H. Eileen Tan, Kelly M. Suino-Powell, Yuanzheng He, Yong Xu, Michael J. Chalmers, et al. 2012. Molecular mimicry regulates ABA signaling by SnRK2 kinases and PP2C phosphatases. Science 335(6064): 85–88. Soon, Fen-Fen, Kelly M. Suino-Powell, Jun Li, Eu-Leong Yong, H. Eric Xu, and Karsten Melcher. 2012. Abscisic acid signaling: thermal stability shift assays as tool to analyze hormone perception and signal transduction. PLoS One 7(10): e47857. Yu, Shanghai, and H. Eric Xu. 2012. Couple dynamics: PPARg and its ligand partners. Structure 20(1): 2–4. Zhou, X. Edward, Fen-Fen Soon, Ley-Moy Ng, Amanda Kovach, Kelly M. Suino-Powell, Jun Li, Eu-Leong Yong, Jian-Kang Zhu, H. Eric Xu, and Karsten Melcher. 2012. Catalytic mechanism and kinase interactions of ABA-signaling PP2C phosphatases. Plant Signaling & Behavior 7(5): 581–588. 72

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