Review
Biochemistry & Molecular Biology
Ning Ma, Anita K. Nivedha, Nagarajan Vaidehi
Summary: GPCRs are membrane-bound proteins that play a critical role in mediating multiple signaling pathways. They possess a dynamic nature and exist in an equilibrium between inactive and active states, with ligands selectively stabilizing specific conformations to shift the equilibrium. This ligand-selective effect is achieved through allosteric communication between the ligand binding site and G protein or beta-arrestin coupling site, allowing for the design of selective ligands and mutants with specific interactions.
Review
Chemistry, Inorganic & Nuclear
Yingxu Wu, Boyu Zhang, Hu Xu, Maomao He, Xiaojing Deng, Linhao Zhang, Qi Dang, Jiangli Fan, Youfei Guan, Xiaojun Peng, Wen Sun
Summary: In 2012, scientists Robert J. Lefkowitz and Brian K. Kobilka won the Nobel Prize for their groundbreaking discovery of the G-protein-coupled receptors (GPCRs), which are responsible for multiple types of cell signaling responses. The design of tools for studying GPCR pharmacology is critical in identifying safer and more effective therapies.
COORDINATION CHEMISTRY REVIEWS
(2023)
Review
Biochemistry & Molecular Biology
Jan Jakubik, Esam E. El-Fakahany
Summary: G-protein coupled receptors (GPCRs) are membrane proteins that transmit extracellular signals to cells, and membrane cholesterol plays a significant role in regulating their function through direct binding and membrane property changes. Cholesterol affects ligand binding and activation of GPCRs, as well as altering their oligomerization state. Manipulating membrane cholesterol levels or modulating cholesterol binding sites on GPCRs may have potential for the development of new therapies.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Multidisciplinary Sciences
Khuraijam Dhanachandra Singh, Zaira P. Jara, Terri Harford, Prasenjit Prasad Saha, Triveni R. Pardhi, Russell Desnoyer, Sadashiva S. Karnik
Summary: This study reports the discovery of allosteric ligands for the AT1R receptor and their potential application in blocking autoimmune antibodies. Through molecular dynamics simulation and high-throughput virtual screening, compounds with a negative allosteric modulator effect on receptor function were identified, demonstrating efficacy in vivo.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Review
Cell Biology
Aiqi Yin, Xiaonian Guan, Jian Zhang, Jianmin Niu
Summary: Preeclampsia is a clinical syndrome characterized by hypertension and proteinuria, and its etiology and pathogenesis are not fully understood. Obesity, immunological diseases, and endocrine metabolic diseases are high-risk factors for preeclampsia. The pathogenesis of preeclampsia involves poor placentation, uteroplacental malperfusion, oxidative stress, immune tolerance dysregulation, vascular inflammation, and endothelial cell dysfunction. The placenta is considered a core factor in the pathogenesis of preeclampsia. G protein-coupled receptors, specifically the secretin/adhesion (Class B) receptors, have potential roles as drug targets in placental development and preeclampsia treatment.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Cell Biology
Jia Duan, Qiufeng Liu, Qingning Yuan, Yujie Ji, Shengnan Zhu, Yangxia Tan, Xinheng He, Youwei Xu, Jingjing Shi, Xi Cheng, Hualiang Jiang, H. Eric Xu, Yi Jiang
Summary: This study reports the cryo-electron microscopy structure of GPR35 coupled with G(13) and bound to the anti-allergic drug lodoxamide. The structure reveals a novel divalent cation coordination site and a unique ionic regulatory mode of GPR35, providing insights into its ligand binding promiscuity. Structural comparison with other G protein subtypes-coupled GPCRs highlights significant movements in the G alpha(13) subunit and the GPR35 TM6 helix.
Article
Cell Biology
Tanveer A. A. Wani, Seema Zargar
Summary: One of the top priorities in medicinal chemistry is the discovery of new molecules that have potential as anticancer agents. Compounds that interact with DNA, such as groove binders, alkylators, and intercalators, have shown promise as chemotherapeutic drugs for cancer treatment. This study focused on the anticancer drug 1,3,5-Tris(4-carboxyphenyl)benzene (H3BTB), which binds to DNA through groove binding and has demonstrated significant cytotoxic potential against breast and cervical cancer cell lines. Computational studies, including molecular docking and molecular dynamics simulations, supported the minor groove binding of H3BTB-DNA complex. This research will contribute to further empirical investigation into the synthesis of metallic and non-metallic derivatives of H3BTB and their potential as bioactive molecules for cancer treatment.
Article
Biochemistry & Molecular Biology
Preeti Jha, Shubhra Chaturvedi, Ruchika Bhat, Nidhi Jain, Anil K. Mishra
Summary: The 5HT1A receptor is crucial in the treatment of depression and anxiety disorders, and the developed homology model shows promise in designing high-affinity probes for these neurological disorders.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Chemistry, Multidisciplinary
Luca Chiesa, Esther Kellenberger
Summary: G protein-coupled receptors play a crucial role in relaying extracellular signals inside the cell. This study proposes a new method based on the conformational dynamics of a protein-ligand complex to improve the selection of ligands with specific pharmacological properties in structure-based virtual screening. Molecular dynamics simulations were used to extract interaction patterns between an agonist and the beta 2 adrenergic receptor, which were then encoded in graphs and used to train a machine learning classifier. The results demonstrate that the consistency of the binding mode during the simulation is important for the success of the method.
JOURNAL OF CHEMINFORMATICS
(2022)
Article
Endocrinology & Metabolism
Ian Winfield, Kerry Barkan, Sarah Routledge, Nathan J. Robertson, Matthew Harris, Ali Jazayeri, John Simms, Christopher A. Reynolds, David R. Poyner, Graham Ladds
Summary: This study investigates the role of the first intracellular loop (ICL1) and the eighth helix (H8) in signal transduction pathways of G protein-coupled receptors (GPCRs). The results suggest that mutations in ICL1 can affect cAMP production and Ca-i(2+) elevation, while having little impact on ERK1/2 activation. Additionally, an insertion in ICL1 is found to switch signaling bias between Ca-i(2+) and cAMP. Molecular dynamics simulations indicate that changes in ICL1 alter the conformation of ICL2 and the H8/TM7 junction.
FRONTIERS IN ENDOCRINOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Rezvan Shahoei, Susheel Pangeni, Matthew A. Sanders, Huamei Zhang, Ljiljana Mladenovic-Lucas, William R. Roush, Geoff Halvorsen, Christopher V. Kelly, James G. Granneman, Yu-ming M. Huang
Summary: In this study, a 3D structure of ABHD5 is successfully built through computational and experimental methods, revealing its binding mechanism with synthetic ligands. Mutations can affect the function of ABHD5, which is of great significance for the development of therapeutic targets for metabolic diseases and cancer.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Biophysics
Chiara Bernard, Angelo Rosario Carotenuto, Nicola Maria Pugno, Massimiliano Fraldi, Luca Deseri
Summary: Cell membranes are dynamic and heterogeneous environments that mediate various biological mechanisms. This study focuses on the theoretical modeling of the spatio-temporal evolution of lipid rafts, ordered lipid microdomains rich in signaling proteins. By coupling diffusive and mechanical phenomena, the researchers aim to explain the co-localization and synergy between protein activation and raft formation. This research provides insights into the remodeling of cell membranes and suggests mechanically based strategies for controlling their selectivity.
BIOMECHANICS AND MODELING IN MECHANOBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Paul T. Kim, Robin Winter, Djork-Arne Clevert
Summary: Research suggests that unsupervised learned representations can predict protein-ligand binding more effectively than handcrafted ones. Various protein and molecule embedding methods have been developed based on different language modeling methods.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemical Research Methods
Mingwei Pang, Wangqiu He, Xufeng Lu, Yuting She, Liangxu Xie, Ren Kong, Shan Chang
Summary: This study proposes a docking method that combines template-based modeling and a scoring function for ligand binding prediction in CASP15. Among the 21 targets, successful predictions were obtained for 14 targets in the top 5 submissions, and partially successful predictions were obtained for 4 targets. Particularly, the method successfully predicted the binding of most ligands for the most complex target, H1114. Analysis of failed systems revealed that conformational changes in the receptor protein may cause large structural deviations in ligand binding prediction. In summary, the hybrid docking scheme efficiently addresses the challenges in ligand binding prediction in CASP15.
BMC BIOINFORMATICS
(2023)
Article
Biochemistry & Molecular Biology
Ugochi H. Isu, Shadi A. Badiee, Ehsaneh Khodadadi, Mahmoud Moradi
Summary: G-protein coupled receptors (GPCRs) play critical roles in various organ systems. Imbalance in cholesterol level affects the structure and function of GPCRs, which is linked to diseases. This review focuses on the interaction, functions, and structural dynamics involved in cholesterol recognition of class C GPCRs.
Article
Endocrinology & Metabolism
S. Yang, X. Xu
JOURNAL OF ENDOCRINOLOGICAL INVESTIGATION
(2022)
Letter
Endocrinology & Metabolism
Shijie Yang, Xiequn Xu
JOURNAL OF CLINICAL ENDOCRINOLOGY & METABOLISM
(2022)
Review
Chemistry, Multidisciplinary
Sarah J. Piper, Rachel M. Johnson, Denise Wootten, Patrick M. Sexton
Summary: Membrane proteins are diverse and present different challenges for structure determination. Previous strategies involved engineering or deconstructing the proteins, but recent advances in biochemistry and cryo-electron microscopy allow for high resolution structure determination of various membrane protein groups.
Review
Biochemistry & Molecular Biology
Jessica Lu, Sarah J. Piper, Peishen Zhao, Laurence J. Miller, Denise Wootten, Patrick M. Sexton
Summary: Pituitary Adenylate Cyclase-Activating Peptide (PACAP) and Vasoactive Intestinal Peptide (VIP) are neuropeptides that play important roles in various physiological and pathological processes by activating specific receptors. The structural similarities between these peptides and their receptors present challenges in designing selective therapeutics.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Pharmacology & Pharmacy
Huong T. M. Nguyen, Emma T. van der Westhuizen, Christopher J. Langmead, Andrew B. Tobin, Patrick M. Sexton, Arthur Christopoulos, Celine Valant
Summary: This review focuses on the drug discovery of M-1 receptor for the treatment of Alzheimer's disease and schizophrenia. Despite some progress, only a few drugs have reached clinical trials due to cholinergic adverse effects.
BRITISH JOURNAL OF PHARMACOLOGY
(2022)
Review
Endocrinology & Metabolism
Brian P. Cary, Xin Zhang, Jianjun Cao, Rachel M. Johnson, Sarah J. Piper, Elliot J. Gerrard, Denise Wootten, Patrick M. Sexton
Summary: G protein-coupled receptors (GPCRs), particularly the B1 class, play a critical role in maintaining homeostasis and are important drug targets. Recent advances in cryo-electron microscopy have provided valuable insights into the structure and dynamics of these receptors, which contribute to our understanding of their functions.
Letter
Endocrinology & Metabolism
Shijie Yang, Meijuan Tan, Feng Gao, Xiequn Xu
JOURNAL OF CLINICAL ENDOCRINOLOGY & METABOLISM
(2023)
Article
Biochemistry & Molecular Biology
Louis Dwomoh, Mario Rossi, Miriam Scarpa, Elham Khajehali, Colin Molloy, Pawel Herzyk, Shailesh N. Mistry, Andrew R. Bottrill, Patrick M. Sexton, Arthur Christopoulos, P. Jeffrey Conn, Craig W. Lindsley, Sophie J. Bradley, Andrew B. Tobin
Summary: Activation of the M-1 receptor may slow the progression of neurodegenerative diseases associated with prion-like misfolded proteins, prolonging survival and maintaining cognitive function in mice with prion diseases.
Article
Multidisciplinary Sciences
Sarah J. Piper, Giuseppe Deganutti, Jessica Lu, Peishen Zhao, Yi-Lynn Liang, Yao Lu, Madeleine M. Fletcher, Mohammed Akhter Hossain, Arthur Christopoulos, Christopher A. Reynolds, Radostin Danev, Patrick M. Sexton, Denise Wootten
Summary: This study uses cryo-EM and MD data to investigate the binding and selectivity of VPAC1R and PAC1R peptide agonists. The findings suggest that the selectivity of VIP for VPAC1R over PAC1R may be due to fewer stable interactions between VIP and VPAC1R compared to PACAP27. This research has important implications for the development of novel selective agonists.
NATURE COMMUNICATIONS
(2022)
Letter
Oncology
Shijie Yang, Meijuan Tan, Feng Gao, Xiequn Xu
JOURNAL OF CLINICAL ONCOLOGY
(2023)
Correction
Biochemistry & Molecular Biology
Alexander S. Powers, Vi Pham, Wessel A. C. Burger, Geoff Thompson, Yianni Laloudakis, Nicholas W. Barnes, Patrick M. Sexton, Steven M. Paul, Arthur Christopoulos, David M. Thal, Christian C. Felder, Celine Valant, Ron O. Dror
NATURE CHEMICAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Alexander S. Powers, Vi Pham, Wessel A. C. Burger, Geoff Thompson, Yianni Laloudakis, Patrick M. Sexton, Steven M. Paul, Arthur Christopoulos, David M. Thal, Christian C. Felder, Celine Valant, Ron O. Dror
Summary: The selectivity of a drug for target receptors is crucial but challenging when the receptors are similar. Serendipitous discovery of ligands that stimulate target receptors more strongly than closely related receptors provides a solution. This study reveals the structural basis for the efficacy-driven selectivity of xanomeline, a clinical drug candidate, between closely related muscarinic acetylcholine receptors (mAChRs), using atomic-level simulations. The results suggest strategies for rational design of ligands achieving efficacy-driven selectivity for G-protein-coupled receptors.
NATURE CHEMICAL BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Wessel A. C. Burger, Vi Pham, Ziva Vuckovic, Alexander S. Powers, Jesse I. Mobbs, Yianni Laloudakis, Alisa Glukhova, Denise Wootten, Andrew B. Tobin, Patrick M. Sexton, Steven M. Paul, Christian C. Felder, Radostin Danev, Ron O. Dror, Arthur Christopoulos, Celine Valant, David M. Thal
Summary: The M4 muscarinic acetylcholine receptor is a significant drug target for the treatment of psychosis, cognition, and addiction. The clinical trial of xanomeline has shown promise in improving symptoms and the cryo-EM structure reveals the binding mechanism, providing insight into its complex pharmacology.
NATURE COMMUNICATIONS
(2023)
Article
Endocrinology & Metabolism
Shijie Yang, Jing Zhan, Xiequn Xu
Summary: The study aims to evaluate the quality of thyroid cancer-related videos on TikTok. The results show that the quality of thyroid cancer information on TikTok is unsatisfactory, indicating a need for high-quality short-video platforms for patient education.
Meeting Abstract
Neurosciences
Wessel A. C. Burger, Vi Pham, Alexander Powers, Ziva Vuckovic, Jesse I. Mobbs, Alisa Glukhova, Denise Wootten, Andrew B. Tobin, Patrick M. Sexton, Steven M. Paul, Christian Felder, Radostin Danev, Arthur Christopoulos, Ron O. Dror, Celine Valant, David M. Thal
NEUROPSYCHOPHARMACOLOGY
(2022)