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Yuan W, Shi X, Lee LTO. RNA therapeutics in targeting G protein-coupled receptors: Recent advances and challenges. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102195. [PMID: 38741614 PMCID: PMC11089380 DOI: 10.1016/j.omtn.2024.102195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
G protein-coupled receptors (GPCRs) are the major targets of existing drugs for a plethora of human diseases and dominate the pharmaceutical market. However, over 50% of the GPCRs remain undruggable. To pursue a breakthrough and overcome this situation, there is significant clinical research for developing RNA-based drugs specifically targeting GPCRs, but none has been approved so far. RNA therapeutics represent a unique and promising approach to selectively targeting previously undruggable targets, including undruggable GPCRs. However, the development of RNA therapeutics faces significant challenges in areas of RNA stability and efficient in vivo delivery. This review presents an overview of the advances in RNA therapeutics and the diverse types of nanoparticle RNA delivery systems. It also describes the potential applications of GPCR-targeted RNA drugs for various human diseases.
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Affiliation(s)
- Wanjun Yuan
- Cancer Centre, Faculty of Health Sciences, University of Macau, Taipa 999078, Macau, China
| | - Xiangyang Shi
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, Shanghai Engineering Research Center of Nano-Biomaterials and Regenerative Medicine, College of Biological Science and Medical Engineering, Donghua University, Shanghai 201620, People’s Republic of China
| | - Leo Tsz On Lee
- Cancer Centre, Faculty of Health Sciences, University of Macau, Taipa 999078, Macau, China
- Ministry of Education Frontiers Science Center for Precision Oncology, University of Macau, Taipa 999078, Macau, China
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2
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Park SY, Kim D, Jung JW, An HJ, Lee J, Park Y, Lee D, Lee S, Kim JM. Targeting class A GPCRs for hard tissue regeneration. Biomaterials 2024; 304:122425. [PMID: 38100905 DOI: 10.1016/j.biomaterials.2023.122425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 12/01/2023] [Accepted: 12/08/2023] [Indexed: 12/17/2023]
Abstract
G protein-coupled receptors (GPCRs) play important roles in various pathogeneses and physiological regulations. Owing to their functional diversity, GPCRs are considered one of the primary pharmaceutical targets. However, drugs targeting GPCRs have not been developed yet to regenerate hard tissues such as teeth and bones. Mesenchymal stromal cells (MSCs) have high proliferation and multi-lineage differentiation potential, which are essential for hard tissue regeneration. Here, we present a strategy for targeting class A GPCRs for hard tissue regeneration by promoting the differentiation of endogenous MSCs into osteogenic and odontogenic progenitor cells. Through in vitro screening targeted at class A GPCRs, we identified six target receptors (LPAR1, F2R, F2RL1, F2RL2, S1PR1, and ADORA2A) and candidate drugs with potent biomineralization effects. Through a combination of profiling whole transcriptome and accessible chromatin regions, we identified that p53 acts as a key transcriptional activator of genes that modulate the biomineralization process. Moreover, the therapeutic potential of class A GPCR-targeting drugs was demonstrated in tooth pulpotomy and calvarial defect models. The selected drugs revealed potent regenerative effects in both tooth and bone defects, represented by newly formed highly mineralized regions. Consequently, this study provides translational evidence for a new regenerative strategy for damaged hard tissue.
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Affiliation(s)
- So Young Park
- Department of Oral Microbiology and Immunology, School of Dentistry and Dental Research Institute, Seoul National University, Seoul, 08826, Republic of Korea
| | - Dohyun Kim
- Department of Conservative Dentistry and Oral Science Research Center, Yonsei University College of Dentistry, Seoul, 03722, Republic of Korea
| | - Ju Won Jung
- Department of Oral Microbiology and Immunology, School of Dentistry and Dental Research Institute, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hyun-Ju An
- Department of Orthopaedic Surgery, CHA Bundang Medical Center, CHA University School of Medicine, Bundang-gu, Seongnam-si, 13496, Republic of Korea
| | - Jaemin Lee
- Department of Orthopaedic Surgery, CHA Bundang Medical Center, CHA University School of Medicine, Bundang-gu, Seongnam-si, 13496, Republic of Korea
| | - Yeji Park
- Department of Conservative Dentistry and Oral Science Research Center, Yonsei University College of Dentistry, Seoul, 03722, Republic of Korea
| | - Dasun Lee
- Department of Conservative Dentistry and Oral Science Research Center, Yonsei University College of Dentistry, Seoul, 03722, Republic of Korea
| | - Soonchul Lee
- Department of Orthopaedic Surgery, CHA Bundang Medical Center, CHA University School of Medicine, Bundang-gu, Seongnam-si, 13496, Republic of Korea.
| | - Jin Man Kim
- Department of Oral Microbiology and Immunology, School of Dentistry and Dental Research Institute, Seoul National University, Seoul, 08826, Republic of Korea.
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3
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Bachari A, Nassar N, Schanknecht E, Telukutla S, Piva TJ, Mantri N. Rationalizing a prospective coupling effect of cannabinoids with the current pharmacotherapy for melanoma treatment. WIREs Mech Dis 2024; 16:e1633. [PMID: 37920964 DOI: 10.1002/wsbm.1633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 09/21/2023] [Accepted: 10/06/2023] [Indexed: 11/04/2023]
Abstract
Melanoma is one of the leading fatal forms of cancer, yet from a treatment perspective, we have minimal control over its reoccurrence and resistance to current pharmacotherapies. The endocannabinoid system (ECS) has recently been accepted as a multifaceted homeostatic regulator, influencing various physiological processes across different biological compartments, including the skin. This review presents an overview of the pathophysiology of melanoma, current pharmacotherapy used for treatment, and the challenges associated with the different pharmacological approaches. Furthermore, it highlights the utility of cannabinoids as an additive remedy for melanoma by restoring the balance between downregulated immunomodulatory pathways and elevated inflammatory cytokines during chronic skin conditions as one of the suggested critical approaches in treating this immunogenic tumor. This article is categorized under: Cancer > Molecular and Cellular Physiology.
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Affiliation(s)
- Ava Bachari
- The Pangenomics Lab, School of Science, RMIT University, Bundoora, Victoria, Australia
| | - Nazim Nassar
- School of Health and Biomedical Sciences, RMIT University, Bundoora, Victoria, Australia
| | - Ellen Schanknecht
- The Pangenomics Lab, School of Science, RMIT University, Bundoora, Victoria, Australia
| | | | - Terrence Jerald Piva
- School of Health and Biomedical Sciences, RMIT University, Bundoora, Victoria, Australia
| | - Nitin Mantri
- The Pangenomics Lab, School of Science, RMIT University, Bundoora, Victoria, Australia
- The UWA Institute of Agriculture, The University of Western Australia, Perth, Western Australia, Australia
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4
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Senapati S, Park PSH. Understanding the Rhodopsin Worldview Through Atomic Force Microscopy (AFM): Structure, Stability, and Activity Studies. CHEM REC 2023; 23:e202300113. [PMID: 37265335 PMCID: PMC10908267 DOI: 10.1002/tcr.202300113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/12/2023] [Indexed: 06/03/2023]
Abstract
Rhodopsin is a G protein-coupled receptor (GPCR) present in the rod outer segment (ROS) of photoreceptor cells that initiates the phototransduction cascade required for scotopic vision. Due to the remarkable advancements in technological tools, the chemistry of rhodopsin has begun to unravel especially over the past few decades, but mostly at the ensemble scale. Atomic force microscopy (AFM) is a tool capable of providing critical information from a single-molecule point of view. In this regard, to bolster our understanding of rhodopsin at the nanoscale level, AFM-based imaging, force spectroscopy, and nano-indentation techniques were employed on ROS disc membranes containing rhodopsin, isolated from vertebrate species both in normal and diseased states. These AFM studies on samples from native retinal tissue have provided fundamental insights into the structure and function of rhodopsin under normal and dysfunctional states. We review here the findings from these AFM studies that provide important insights on the supramolecular organization of rhodopsin within the membrane and factors that contribute to this organization, the molecular interactions stabilizing the structure of the receptor and factors that can modify those interactions, and the mechanism underlying constitutive activity in the receptor that can cause disease.
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Affiliation(s)
- Subhadip Senapati
- Department of Ophthalmology and Visual Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
- Prayoga Institute of Education Research, Bengaluru, KA 560116, India
| | - Paul S-H Park
- Department of Ophthalmology and Visual Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
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Lees JA, Dias JM, Rajamohan F, Fortin JP, O'Connor R, Kong JX, Hughes EAG, Fisher EL, Tuttle JB, Lovett G, Kormos BL, Unwalla RJ, Zhang L, Dechert Schmitt AM, Zhou D, Moran M, Stevens KA, Fennell KF, Varghese AE, Maxwell A, Cote EE, Zhang Y, Han S. An inverse agonist of orphan receptor GPR61 acts by a G protein-competitive allosteric mechanism. Nat Commun 2023; 14:5938. [PMID: 37741852 PMCID: PMC10517971 DOI: 10.1038/s41467-023-41646-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 09/11/2023] [Indexed: 09/25/2023] Open
Abstract
GPR61 is an orphan GPCR related to biogenic amine receptors. Its association with phenotypes relating to appetite makes it of interest as a druggable target to treat disorders of metabolism and body weight, such as obesity and cachexia. To date, the lack of structural information or a known biological ligand or tool compound has hindered comprehensive efforts to study GPR61 structure and function. Here, we report a structural characterization of GPR61, in both its active-like complex with heterotrimeric G protein and in its inactive state. Moreover, we report the discovery of a potent and selective small-molecule inverse agonist against GPR61 and structural elucidation of its allosteric binding site and mode of action. These findings offer mechanistic insights into an orphan GPCR while providing both a structural framework and tool compound to support further studies of GPR61 function and modulation.
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Affiliation(s)
- Joshua A Lees
- Discovery Sciences, Medicine Design, Pfizer Inc., Groton, CT, USA
| | - João M Dias
- Discovery Sciences, Medicine Design, Pfizer Inc., Groton, CT, USA
| | | | | | - Rebecca O'Connor
- Discovery Sciences, Medicine Design, Pfizer Inc., Groton, CT, USA
| | - Jimmy X Kong
- Internal Medicine Research Unit, Pfizer Inc., Cambridge, MA, USA
| | - Emily A G Hughes
- Internal Medicine Research Unit, Pfizer Inc., Cambridge, MA, USA
| | - Ethan L Fisher
- Internal Medicine, Medicine Design, Pfizer Inc., Groton, CT, USA
| | - Jamison B Tuttle
- Internal Medicine, Medicine Design, Pfizer Inc., Cambridge, MA, USA
| | - Gabrielle Lovett
- Internal Medicine, Medicine Design, Pfizer Inc., Cambridge, MA, USA
| | - Bethany L Kormos
- Internal Medicine, Medicine Design, Pfizer Inc., Cambridge, MA, USA
| | | | - Lei Zhang
- Internal Medicine, Medicine Design, Pfizer Inc., Cambridge, MA, USA
| | | | - Dahui Zhou
- Internal Medicine, Medicine Design, Pfizer Inc., Groton, CT, USA
| | - Michael Moran
- Internal Medicine, Medicine Design, Pfizer Inc., Groton, CT, USA
| | | | | | | | - Andrew Maxwell
- Discovery Sciences, Medicine Design, Pfizer Inc., Groton, CT, USA
| | - Emmaline E Cote
- Discovery Sciences, Medicine Design, Pfizer Inc., Groton, CT, USA
| | - Yuan Zhang
- Internal Medicine, Medicine Design, Pfizer Inc., Cambridge, MA, USA
| | - Seungil Han
- Discovery Sciences, Medicine Design, Pfizer Inc., Groton, CT, USA.
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6
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Cosarderelioglu C, Kreimer S, Plaza‐Rodriguez AI, Iglesias PA, Talbot CC, Siragy HM, Carey RM, Ubaida‐Mohien C, O'Rourke B, Ferrucci L, Bennett DA, Walston J, Abadir P. Decoding Angiotensin Receptors: TOMAHAQ-Based Detection and Quantification of Angiotensin Type-1 and Type-2 Receptors. J Am Heart Assoc 2023; 12:e030791. [PMID: 37681524 PMCID: PMC10547273 DOI: 10.1161/jaha.123.030791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 07/20/2023] [Indexed: 09/09/2023]
Abstract
Background The renin-angiotensin system plays a crucial role in human physiology, and its main hormone, angiotensin, activates 2 G-protein-coupled receptors, the angiotensin type-1 and type-2 receptors, in almost every organ. However, controversy exists about the location, distribution, and expression levels of these receptors. Concerns have been raised over the low sensitivity, low specificity, and large variability between lots of commercially available antibodies for angiotensin type-1 and type-2 receptors, which makes it difficult to reconciliate results of different studies. Here, we describe the first non-antibody-based sensitive and specific targeted quantitative mass spectrometry assay for angiotensin receptors. Methods and Results Using a technique that allows targeted analysis of multiple peptides across multiple samples in a single mass spectrometry analysis, known as TOMAHAQ (triggered by offset, multiplexed, accurate mass, high resolution, and absolute quantification), we have identified and validated specific human tryptic peptides that permit identification and quantification of angiotensin type-1 and type-2 receptors in biological samples. Several peptide sequences are conserved in rodents, making these mass spectrometry assays amenable to both preclinical and clinical studies. We have used this method to quantify angiotensin type-1 and type-2 receptors in postmortem frontal cortex samples of older adults (n=28) with Alzheimer dementia. We correlated levels of angiotensin receptors to biomarkers classically linked to renin-angiotensin system activation, including oxidative stress, inflammation, amyloid-β load, and paired helical filament-tau tangle burden. Conclusions These robust high-throughput assays will not only catalyze novel mechanistic studies in the angiotensin research field but may also help to identify patients with an unbalanced angiotensin receptor distribution who would benefit from angiotensin receptor blocker treatment.
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Affiliation(s)
- Caglar Cosarderelioglu
- Division of Geriatric Medicine and GerontologyJohns Hopkins University School of MedicineBaltimoreMD
- Division of Geriatrics, Department of Internal MedicineAnkara University School of MedicineAnkaraTurkey
| | - Simion Kreimer
- The Mass Spectrometry and Proteomics FacilityJohns Hopkins University School of MedicineBaltimoreMD
| | | | - Pablo A. Iglesias
- Department of Electrical and Computer Engineering, Whiting School of EngineeringJohns Hopkins UniversityBaltimoreMD
| | - C. Conover Talbot
- Institute for Basic Biomedical Sciences, Johns Hopkins University School of MedicineBaltimoreMD
| | - Helmy M. Siragy
- Division of Endocrinology and Metabolism, Department of MedicineUniversity of VirginiaCharlottesvilleVA
| | - Robert M. Carey
- Division of Endocrinology and Metabolism, Department of MedicineUniversity of VirginiaCharlottesvilleVA
| | | | - Brian O'Rourke
- Division of Cardiology, Department of MedicineJohns Hopkins UniversityBaltimoreMD
| | - Luigi Ferrucci
- National Institute on Aging, National Institutes of HealthBaltimoreMD
| | - David A. Bennett
- Rush Alzheimer’s Disease CenterRush University Medical CenterChicagoIL
| | - Jeremy Walston
- Division of Geriatric Medicine and GerontologyJohns Hopkins University School of MedicineBaltimoreMD
| | - Peter Abadir
- Division of Geriatric Medicine and GerontologyJohns Hopkins University School of MedicineBaltimoreMD
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7
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Dutta Gupta O, Karbat I, Pal K. Understanding the Molecular Regulation of Serotonin Receptor 5-HTR 1B-β-Arrestin1 Complex in Stress and Anxiety Disorders. J Mol Neurosci 2023; 73:664-677. [PMID: 37580644 DOI: 10.1007/s12031-023-02146-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 07/31/2023] [Indexed: 08/16/2023]
Abstract
The serotonin receptor subtype 5-HTR1B is widely distributed in the brain with an important role in various behavioral implications including neurological conditions and psychiatric disorders. The neuromodulatory action of 5-HTR1B largely depends upon its arrestin mediated signaling pathway. In this study, we tried to investigate the role of unusually long intracellular loop 3 (ICL3) region of the serotonin receptor 5-HTR1B in interaction with β-arrestin1 (Arr2) to compensate for the absence of the long cytoplasmic tail. Molecular modeling and docking tools were employed to obtain a suitable molecular conformation of the ICL3 region in complex with Arr2 which dictates the specific complex formation of 5-HTR1B with Arr2. This reveals the novel molecular mechanism of phosphorylated ICL3 mediated GPCR-arrestin interaction in the absence of the long cytoplasmic tail. The in-cell disulfide cross-linking experiments and molecular dynamics simulations of the complex further validate the model of 5-HTR1B-ICL3-Arr2 complex. Two serine residues (Ser281 and Ser295) within the 5-HTR1B-ICL3 region were found to be occupying the electropositive pocket of Arr2 in our model and might be crucial for phosphorylation and specific Arr2 binding. The alignment studies of these residues showed them to be conserved only across 5-HTR1B mammalian species. Thus, our studies were able to predict a molecular conformation of 5-HTR1B-Arr2 and identify the role of long ICL3 in the signaling process which might be crucial in designing targeted drugs (biased agonists) that promote GPCR-Arr2 signaling to deter the effects of stress and anxiety-like disorders.
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Affiliation(s)
- Oindrilla Dutta Gupta
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, 700126, Kolkata, West Bengal, India
| | - Izhar Karbat
- Department of Biomolecular Sciences, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Kuntal Pal
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, 700126, Kolkata, West Bengal, India.
- School of Biosciences and Technology (SBST), Vellore Institute of Technology, 632014, Vellore, Tamil Nadu, India.
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8
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Isu UH, Badiee SA, Khodadadi E, Moradi M. Cholesterol in Class C GPCRs: Role, Relevance, and Localization. MEMBRANES 2023; 13:301. [PMID: 36984688 PMCID: PMC10056374 DOI: 10.3390/membranes13030301] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 02/21/2023] [Accepted: 02/28/2023] [Indexed: 06/18/2023]
Abstract
G-protein coupled receptors (GPCRs), one of the largest superfamilies of cell-surface receptors, are heptahelical integral membrane proteins that play critical roles in virtually every organ system. G-protein-coupled receptors operate in membranes rich in cholesterol, with an imbalance in cholesterol level within the vicinity of GPCR transmembrane domains affecting the structure and/or function of many GPCRs, a phenomenon that has been linked to several diseases. These effects of cholesterol could result in indirect changes by altering the mechanical properties of the lipid environment or direct changes by binding to specific sites on the protein. There are a number of studies and reviews on how cholesterol modulates class A GPCRs; however, this area of study is yet to be explored for class C GPCRs, which are characterized by a large extracellular region and often form constitutive dimers. This review highlights specific sites of interaction, functions, and structural dynamics involved in the cholesterol recognition of the class C GPCRs. We summarize recent data from some typical family members to explain the effects of membrane cholesterol on the structural features and functions of class C GPCRs and speculate on their corresponding therapeutic potential.
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9
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Gulati S, Palczewski K. Structural view of G protein-coupled receptor signaling in the retinal rod outer segment. Trends Biochem Sci 2023; 48:172-186. [PMID: 36163145 PMCID: PMC9868064 DOI: 10.1016/j.tibs.2022.08.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 08/26/2022] [Accepted: 08/29/2022] [Indexed: 01/26/2023]
Abstract
Visual phototransduction is the most extensively studied G protein-coupled receptor (GPCR) signaling pathway because of its quantifiable stimulus, non-redundancy of genes, and immense importance in vision. We summarize recent discoveries that have advanced our understanding of rod outer segment (ROS) morphology and the pathological basis of retinal diseases. We have combined recently published cryo-electron tomography (cryo-ET) data on the ROS with structural knowledge on individual proteins to define the precise spatial limitations under which phototransduction occurs. Although hypothetical, the reconstruction of the rod phototransduction system highlights the potential roles of phosphodiesterase 6 (PDE6) and guanylate cyclases (GCs) in maintaining the spacing between ROS discs, suggesting a plausible mechanism by which intrinsic optical signals are generated in the retina.
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Affiliation(s)
| | - Krzysztof Palczewski
- Gavin Herbert Eye Institute and the Department of Ophthalmology, Center for Translational Vision Research, Department of Physiology and Biophysics, Department of Chemistry, Molecular Biology, and Biochemistry, University of California Irvine, 850 Health Sciences Road, Irvine, CA 92697-4375, USA.
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10
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Tricomi J, Landini L, Nieddu V, Cavallaro U, Baker JG, Papakyriakou A, Richichi B. Rational design, synthesis, and pharmacological evaluation of a cohort of novel beta-adrenergic receptors ligands enables an assessment of structure-activity relationships. Eur J Med Chem 2023; 246:114961. [PMID: 36495629 DOI: 10.1016/j.ejmech.2022.114961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 11/14/2022] [Accepted: 11/22/2022] [Indexed: 11/30/2022]
Abstract
Biomedical applications of molecules that are able to modulate β-adrenergic signaling have become increasingly attractive over the last decade, revealing that β-adrenergic receptors (β-ARs) are key targets for a plethora of therapeutic interventions, including cancer. Despite successes in β-AR drug discovery, identification of β-AR ligands that are useful as selective chemical tools in pharmacological studies of the three β-AR subtypes, or lead compounds for drug development is still a highly challenging task. This is mainly due to the intrinsic plasticity of β-ARs as G protein-coupled receptors in conjunction with the requirement for functional receptor subtype selectivity, tissue specificity and minimal off-target effects. With the aim to provide insight into structure-activity relationships for the three β-AR subtypes, we have synthesized and obtained the pharmacological profile of a series of structurally diverse compounds (named MC) that were designed based on the aryloxy-propanolamine scaffold of SR59230A. Comparative analysis of their predicted binding mode within the active and inactive states of the receptors in combination with their pharmacological profile revealed key structural elements that control their activity as agonists or antagonists, in addition to clues about substituents that mediate selectivity for one receptor subtype over the others. We anticipate that these results will facilitate selective β-AR drug development efforts.
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Affiliation(s)
- Jacopo Tricomi
- Department of Chemistry, University of Firenze, Via della Lastruccia 13, 50019 Sesto Fiorentino, Firenze, Italy
| | - Luca Landini
- Department of Chemistry, University of Firenze, Via della Lastruccia 13, 50019 Sesto Fiorentino, Firenze, Italy; Institute of Biosciences and Applications, National Centre for Scientific Research "Demokritos", 15341 Agia Paraskevi, Athens, Greece
| | - Valentina Nieddu
- Unit of Gynaecological Oncology Research, European Institute of Oncology IRCCS, Milan, Italy
| | - Ugo Cavallaro
- Unit of Gynaecological Oncology Research, European Institute of Oncology IRCCS, Milan, Italy
| | - Jillian G Baker
- Cell Signalling Research Group, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Athanasios Papakyriakou
- Institute of Biosciences and Applications, National Centre for Scientific Research "Demokritos", 15341 Agia Paraskevi, Athens, Greece.
| | - Barbara Richichi
- Department of Chemistry, University of Firenze, Via della Lastruccia 13, 50019 Sesto Fiorentino, Firenze, Italy.
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Pasquaré SJ, Chamorro-Aguirre E, Gaveglio VL. The endocannabinoid system in the visual process. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY 2022. [DOI: 10.1016/j.jpap.2022.100159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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12
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Chen X, Yuan Y, Chen Y, Yu J, Wang J, Chen J, Guo Y, Pu X. Biased Activation Mechanism Induced by GPCR Heterodimerization: Observations from μOR/δOR Dimers. J Chem Inf Model 2022; 62:5581-5600. [PMID: 36377848 DOI: 10.1021/acs.jcim.2c00962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
GPCRs regulate multiple intracellular signaling cascades. Biasedly activating one signaling pathway over the others provides additional clinical utility to optimize GPCR-based therapies. GPCR heterodimers possess different functions from their monomeric states, including their selectivity to different transducers. However, the biased signaling mechanism induced by the heterodimerization remains unclear. Motivated by the issue, we select an important GPCR heterodimer (μOR/δOR heterodimer) as a case and use microsecond Gaussian accelerated molecular dynamics simulation coupled with potential of mean force and protein structure network (PSN) to probe mechanisms regarding the heterodimerization-induced constitutive β-arrestin activity and efficacy change of the agonist DAMGO. The results show that only the lowest energy state of the μOR/δOR heterodimer, which adopts a slightly outward shift of TM6 and an ICL2 conformation close to the receptor core, can selectively accommodate β-arrestins. PSN further reveals important roles of H8, ICL1, and ICL2 in regulating the constitutive β-arrestin-biased activity for the apo μOR/δOR heterodimer. In addition, the heterodimerization can allosterically alter the binding mode of DAMGO mainly by means of W7.35. Consequently, DAMGO transmits the structural signal mainly through TM6 and TM7 in the dimer, rather than TM3 similar to the μOR monomer, thus changing the efficacy of DAMGO from a balanced agonist to the β-arrestin-biased one. On the other side, the binding of DAMGO to the heterodimer can stabilize μOR/δOR heterodimers through a stronger interaction of TM1/TM1 and H8/H8, accordingly enhancing the interaction of μOR with δOR and the binding affinity of the dimer to the β-arrestin. The agonist DAMGO does not change main compositions of the regulation network from the dimer interface to the transducer binding pocket of the μOR protomer, but induces an increase in the structural communication of the network, which should contribute to the enhanced β-arrestin coupling. Our observations, for the first time, reveal the molecular mechanism of the biased signaling induced by the heterodimerization for GPCRs, which should be beneficial to more comprehensively understand the GPCR bias signaling.
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Affiliation(s)
- Xin Chen
- College of Chemistry, Sichuan University, Chengdu610064, China
| | - Yuan Yuan
- College of Management, Southwest University for Nationalities, Chengdu610041, China
| | - Yichi Chen
- College of Chemistry, Sichuan University, Chengdu610064, China
| | - Jin Yu
- Department of Physics and Astronomy, University of California, Irvine, California92697, United States
| | - Jingzhou Wang
- College of Chemistry, Sichuan University, Chengdu610064, China
| | - Jianfang Chen
- College of Chemistry, Sichuan University, Chengdu610064, China
| | - Yanzhi Guo
- College of Chemistry, Sichuan University, Chengdu610064, China
| | - Xuemei Pu
- College of Chemistry, Sichuan University, Chengdu610064, China
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G Protein-coupled Receptor (GPCR) Reconstitution and Labeling for Solution Nuclear Magnetic Resonance (NMR) Studies of the Structural Basis of Transmembrane Signaling. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27092658. [PMID: 35566006 PMCID: PMC9101874 DOI: 10.3390/molecules27092658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/14/2022] [Accepted: 04/14/2022] [Indexed: 11/17/2022]
Abstract
G protein-coupled receptors (GPCRs) are a large membrane protein family found in higher organisms, including the human body. GPCRs mediate cellular responses to diverse extracellular stimuli and thus control key physiological functions, which makes them important targets for drug design. Signaling by GPCRs is related to the structure and dynamics of these proteins, which are modulated by extrinsic ligands as well as by intracellular binding partners such as G proteins and arrestins. Here, we review some basics of using nuclear magnetic resonance (NMR) spectroscopy in solution for the characterization of GPCR conformations and intermolecular interactions that relate to transmembrane signaling.
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14
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Ippolito M, De Pascali F, Inoue A, Benovic JL. Phenylalanine 193 in Extracellular Loop 2 of the β 2-Adrenergic Receptor Coordinates β-Arrestin Interaction. Mol Pharmacol 2022; 101:87-94. [PMID: 34853152 PMCID: PMC8969133 DOI: 10.1124/molpharm.121.000332] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 11/21/2021] [Indexed: 02/03/2023] Open
Abstract
G protein-coupled receptors (GPCRs) transduce a diverse variety of extracellular stimuli into intracellular signaling. These receptors are the most clinically productive drug targets at present. Despite decades of research on the signaling consequences of molecule-receptor interactions, conformational components of receptor-effector interactions remain incompletely described. The β 2-adrenergic receptor (β 2AR) is a prototypical and extensively studied GPCR that can provide insight into this aspect of GPCR signaling thanks to robust structural data and rich pharmacopeia. Using bioluminescence resonance energy transfer -based biosensors, second messenger assays, and biochemical techniques, we characterize the properties of β 2AR-F193A. This single point mutation in extracellular loop 2 of the β 2AR is sufficient to intrinsically bias the β 2AR away from β-arrestin interaction and demonstrates altered regulatory outcomes downstream of this functional selectivity. This study highlights the importance of extracellular control of intracellular response to stimuli and suggests a previously undescribed role for the extracellular loops of the receptor and the extracellular pocket formed by transmembrane domains 2, 3, and 7 in GPCR regulation that may contribute to biased signaling at GPCRs. SIGNIFICANCE STATEMENT: The role of extracellular G protein-coupled receptor (GPCR) domains in mediating intracellular interactions is poorly understood. We characterized the effects of extracellular loop mutations on agonist-promoted interactions of GPCRs with G protein and β-arrestin. Our studies reveal that F193 in extracellular loop 2 in the β2-adrenergic receptor mediates interactions with G protein and β-arrestin with a biased loss of β-arrestin binding. These results provide new insights on the role of the extracellular domain in differentially modulating intracellular interactions with GPCRs.
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Affiliation(s)
- Michael Ippolito
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, (M.I., F.D.P., J.L.B.); and Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan (A.I.)
| | - Francesco De Pascali
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, (M.I., F.D.P., J.L.B.); and Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan (A.I.)
| | - Asuka Inoue
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, (M.I., F.D.P., J.L.B.); and Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan (A.I.)
| | - Jeffrey L Benovic
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, (M.I., F.D.P., J.L.B.); and Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan (A.I.)
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15
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Berntsen HF, Bodin J, Øvrevik J, Berntsen CF, Østby GC, Brinchmann BC, Ropstad E, Myhre O. A human relevant mixture of persistent organic pollutants induces reactive oxygen species formation in isolated human leucocytes: Involvement of the β2-adrenergic receptor. ENVIRONMENT INTERNATIONAL 2022; 158:106900. [PMID: 34607039 DOI: 10.1016/j.envint.2021.106900] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 09/17/2021] [Accepted: 09/22/2021] [Indexed: 06/13/2023]
Abstract
Exposure to chlorinated (Cl), brominated (Br) and perfluoroalkyl acid (PFAA) persistent organic pollutants (POPs) is associated with immunotoxicity and other adverse effects in humans and animals. Previous studies on POPs have mainly focused on single chemicals, while studies on complex mixtures are limited. Using DCF and luminol assays we examined effects on ROS generation in isolated human neutrophils, monocytes and lymphocytes, after in vitro exposure to a total mixture and sub-mixtures of 29 persistent compounds (Cl, Br, and PFAA). The mixtures were based on compounds prominent in blood, breast milk, and/or food. All mixture combinations induced ROS production in one or several of the cell models, and in some cases even at concentrations corresponding to human blood levels (compound range 1 pM - 16 nM). Whilst some interactions were detected (assessed using a mixed linear model), halogenated subgroups mainly acted additively. Mechanistic studies in neutrophils at 500× human levels (0.5 nM - 8 µM) indicated similar mechanisms of action for the Cl, PFAA, the combined PFAA + Cl and total (PFAA + Br + Cl) mixtures, and ROS responses appeared to involve β2-adrenergic receptor (β2AR) and Ca2+ signalling, as well as activation of NADPH oxidases. In line with this, the total mixture also increased cyclic AMP at levels comparable with the non-selective βAR agonist, isoproterenol. Although the detailed mechanisms involved in these responses remain to be elucidated, our data show that POP mixtures at concentrations found in human blood, may trigger stress responses in circulating immune cells. Mixtures of POPs, further seemed to interfere with adrenergic pathways, indicating a novel role of βARs in POP-induced effects.
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Affiliation(s)
- Hanne Friis Berntsen
- Department of Production Animal Clinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, P.O. Box 5003 NMBU, NO-1432 Ås, Norway; National Institute of Occupational Health, P.O. Box 5330, Majorstuen, 0304 Oslo, Norway.
| | - Johanna Bodin
- Department of Methods Development and Analytics, Norwegian Institute of Public Health, N-0456 Oslo, Norway.
| | - Johan Øvrevik
- Department of Environmental Health, Norwegian Institute of Public Health, N-0456 Oslo, Norway; Department of Biosciences, University of Oslo, Norway.
| | - Christopher Friis Berntsen
- Department of Internal Medicine, Sykehuset Innlandet Hospital Trust, Gjøvik, Norway; Department of Internal Medicine, Lovisenberg Diaconal Hospital, Oslo, Norway.
| | - Gunn C Østby
- Department of Production Animal Clinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, P.O. Box 5003 NMBU, NO-1432 Ås, Norway.
| | - Bendik C Brinchmann
- National Institute of Occupational Health, P.O. Box 5330, Majorstuen, 0304 Oslo, Norway; Department of Environmental Health, Norwegian Institute of Public Health, N-0456 Oslo, Norway.
| | - Erik Ropstad
- Department of Production Animal Clinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, P.O. Box 5003 NMBU, NO-1432 Ås, Norway.
| | - Oddvar Myhre
- Department of Environmental Health, Norwegian Institute of Public Health, N-0456 Oslo, Norway.
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16
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Lees JA, Dias JM, Han S. Applications of Cryo-EM in small molecule and biologics drug design. Biochem Soc Trans 2021; 49:2627-2638. [PMID: 34812853 PMCID: PMC8786282 DOI: 10.1042/bst20210444] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/22/2021] [Accepted: 10/27/2021] [Indexed: 02/03/2023]
Abstract
Electron cryo-microscopy (cryo-EM) is a powerful technique for the structural characterization of biological macromolecules, enabling high-resolution analysis of targets once inaccessible to structural interrogation. In recent years, pharmaceutical companies have begun to utilize cryo-EM for structure-based drug design. Structural analysis of integral membrane proteins, which comprise a large proportion of druggable targets and pose particular challenges for X-ray crystallography, by cryo-EM has enabled insights into important drug target families such as G protein-coupled receptors (GPCRs), ion channels, and solute carrier (SLCs) proteins. Structural characterization of biologics, such as vaccines, viral vectors, and gene therapy agents, has also become significantly more tractable. As a result, cryo-EM has begun to make major impacts in bringing critical therapeutics to market. In this review, we discuss recent instructive examples of impacts from cryo-EM in therapeutics design, focusing largely on its implementation at Pfizer. We also discuss the opportunities afforded by emerging technological advances in cryo-EM, and the prospects for future development of the technique.
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Affiliation(s)
- Joshua A. Lees
- Discovery Sciences, Medicine Design, Pfizer Worldwide Research and Development, Groton, CT 06340, U.S.A
| | - Joao M. Dias
- Discovery Sciences, Medicine Design, Pfizer Worldwide Research and Development, Groton, CT 06340, U.S.A
| | - Seungil Han
- Discovery Sciences, Medicine Design, Pfizer Worldwide Research and Development, Groton, CT 06340, U.S.A
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17
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Pal A, Curtin JF, Kinsella GK. Structure based prediction of a novel GPR120 antagonist based on pharmacophore screening and molecular dynamics simulations. Comput Struct Biotechnol J 2021; 19:6050-6063. [PMID: 34849208 PMCID: PMC8605389 DOI: 10.1016/j.csbj.2021.11.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 11/03/2021] [Accepted: 11/03/2021] [Indexed: 12/20/2022] Open
Abstract
Hypothesis of the important residues in conserving the GPR120S “ionic-lock”. Computational model targeting W277 and N313 for virtual screening of GPR120S ligands. Cpd 9 emerged as a potential GPR120S antagonist and anti-cancer treatment.
The G-protein coupled receptor, GPR120, has ubiquitous expression and multifaceted roles in modulating metabolic and anti-inflammatory processes. Recent implications of its role in cancer progression have presented GPR120 as an attractive oncogenic drug target. GPR120 gene knockdown in breast cancer studies revealed a role of GPR120-induced chemoresistance in epirubicin and cisplatin-induced DNA damage in tumour cells. Higher expression and activation levels of GPR120 is also reported to promote tumour angiogenesis and cell migration in colorectal cancer. Some agonists targeting GPR120 have been reported, such as TUG891 and Compound39, but to date development of small-molecule inhibitors of GPR120 is limited. Herein, following homology modelling of the receptor a pharmacophore hypothesis was derived from 300 ns all-atomic molecular dynamics (MD) simulations on apo, TUG891-bound and Compound39-bound GPR120S (short isoform) receptor models embedded in a water solvated lipid bilayer system. We performed comparative MD analysis on protein–ligand interactions between the two agonist and apo simulations on the stability of the “ionic lock” – a Class A GPCRs characteristic of receptor activation and inactivation. The detailed analysis predicted that ligand interactions with W277 and N313 are critical to conserve the “ionic-lock” conformation (R136 of Helix 3) and prevent GPR120S receptor activation. The results led to generation of a W277 and N313 focused pharmacophore hypothesis and the screening of the ZINC15 database using ZINCPharmer through the structure-based pharmacophore. 100 ns all-atomic molecular dynamics (MD) simulations were performed on 9 small molecules identified and Cpd 9, (2-hydroxy-N-{4-[(6-hydroxy-2-methylpyrimidin-4-yl) amino] phenyl} benzamide) was predicted to be a small-molecule GPR120S antagonist. The conformational results from the collective all-atomic MD analysis provided structural information for further identification and optimisation of novel druggable inhibitors of GPR120S using this rational design approach, which could have future potential for anti-cancer drug development studies.
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Affiliation(s)
- Ajay Pal
- School of Food Science and Environmental Health, College of Sciences and Health, Technological University Dublin, Dublin D07 ADY7, Ireland.,Environmental Sustainability and Health Institute (ESHI), Grangegorman, Technological University Dublin, Dublin D07 H6K8, Ireland
| | - James F Curtin
- School of Food Science and Environmental Health, College of Sciences and Health, Technological University Dublin, Dublin D07 ADY7, Ireland
| | - Gemma K Kinsella
- School of Food Science and Environmental Health, College of Sciences and Health, Technological University Dublin, Dublin D07 ADY7, Ireland
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18
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Wu WJ, Xia CL, Ou SJ, Yang Y, Ma YF, Hou YL, Yang QP, Zhang J, Li JW, Qi Y, Xu CP. Novel Elongator Protein 2 Inhibitors Mitigating Tumor Necrosis Factor- α Induced Osteogenic Differentiation Inhibition. BIOMED RESEARCH INTERNATIONAL 2021; 2021:3664564. [PMID: 34853789 PMCID: PMC8629650 DOI: 10.1155/2021/3664564] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 10/12/2021] [Indexed: 11/17/2022]
Abstract
Tumor necrosis factor-α is a common cytokine that increases in inflammatory processes, slows the differentiation of bone formation, and induces osteodystrophy in the long-term inflammatory microenvironment. Our previous study confirmed that the Elongation protein 2 (ELP2) plays a significant role in osteogenesis and osteogenic differentiation, which is considered a drug discovery target in diseases related to bone formation and differentiation. In this study, we applied an in silico virtual screening method to select molecules that bind to the ELP2 protein from a chemical drug molecule library and obtained 95 candidates. Then, we included 11 candidates by observing the docking patterns and the noncovalent bonds. The binding affinity of the ELP2 protein with the candidate compounds was examined by SPR analysis, and 5 out of 11 compounds performed good binding affinity to the mouse ELP2 protein. After in vitro cell differentiation assay, candidates 2# and 5# were shown to reduce differentiation inhibition after tumor necrosis factor-α stimulation, allowing further optimization and development for potential clinical treatment of inflammation-mediated orthopedic diseases.
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Affiliation(s)
- Wen-Jiao Wu
- Department of Medical Research Center, Guangdong Second Provincial General Hospital, Guangzhou, Guangdong, China
| | - Chang-Liang Xia
- Department of Orthopaedics, Guangdong Second Provincial General Hospital, Guangzhou, Guangdong, China
| | - Shuan-Ji Ou
- Department of Orthopaedics, Guangdong Second Provincial General Hospital, Guangzhou, Guangdong, China
| | - Yang Yang
- Department of Orthopaedics, Guangdong Second Provincial General Hospital, Guangzhou, Guangdong, China
| | - Yun-Fei Ma
- Department of Orthopaedics and Traumatology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Yi-Long Hou
- Department of Orthopaedics and Traumatology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Qing-Po Yang
- Department of Orthopaedics, The First People's Hospital of Kashgar Prefecture, Kashgar, Xinjiang, China
| | - Jun Zhang
- Department of Orthopaedics, The First People's Hospital of Kashgar Prefecture, Kashgar, Xinjiang, China
| | - Jian-Wei Li
- Department of Orthopaedics, Shenzhen Shekou People's Hospital, Shenzhen, Guangdong, China
| | - Yong Qi
- Department of Orthopaedics, Guangdong Second Provincial General Hospital, Guangzhou, Guangdong, China
| | - Chang-Peng Xu
- Department of Orthopaedics, Guangdong Second Provincial General Hospital, Guangzhou, Guangdong, China
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19
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Islam MA, Rallabandi VPS, Mohammed S, Srinivasan S, Natarajan S, Dudekula DB, Park J. Screening of β1- and β2-Adrenergic Receptor Modulators through Advanced Pharmacoinformatics and Machine Learning Approaches. Int J Mol Sci 2021; 22:11191. [PMID: 34681845 PMCID: PMC8538848 DOI: 10.3390/ijms222011191] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 10/14/2021] [Accepted: 10/14/2021] [Indexed: 12/15/2022] Open
Abstract
Cardiovascular diseases (CDs) are a major concern in the human race and one of the leading causes of death worldwide. β-Adrenergic receptors (β1-AR and β2-AR) play a crucial role in the overall regulation of cardiac function. In the present study, structure-based virtual screening, machine learning (ML), and a ligand-based similarity search were conducted for the PubChem database against both β1- and β2-AR. Initially, all docked molecules were screened using the threshold binding energy value. Molecules with a better binding affinity were further used for segregation as active and inactive through ML. The pharmacokinetic assessment was carried out on molecules retained in the above step. Further, similarity searching of the ChEMBL and DrugBank databases was performed. From detailed analysis of the above data, four compounds for each of β1- and β2-AR were found to be promising in nature. A number of critical ligand-binding amino acids formed potential hydrogen bonds and hydrophobic interactions. Finally, a molecular dynamics (MD) simulation study of each molecule bound with the respective target was performed. A number of parameters obtained from the MD simulation trajectories were calculated and substantiated the stability between the protein-ligand complex. Hence, it can be postulated that the final molecules might be crucial for CDs subjected to experimental validation.
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Affiliation(s)
- Md Ataul Islam
- 3BIGS Omicscore Pvt. Ltd., 1, O Shaughnessy Rd, Langford Gardens, Bengaluru, Karnataka 560025, India; (M.A.I.); (V.P.S.R.); (S.M.); (S.S.); (D.B.D.)
| | - V. P. Subramanyam Rallabandi
- 3BIGS Omicscore Pvt. Ltd., 1, O Shaughnessy Rd, Langford Gardens, Bengaluru, Karnataka 560025, India; (M.A.I.); (V.P.S.R.); (S.M.); (S.S.); (D.B.D.)
| | - Sameer Mohammed
- 3BIGS Omicscore Pvt. Ltd., 1, O Shaughnessy Rd, Langford Gardens, Bengaluru, Karnataka 560025, India; (M.A.I.); (V.P.S.R.); (S.M.); (S.S.); (D.B.D.)
| | - Sridhar Srinivasan
- 3BIGS Omicscore Pvt. Ltd., 1, O Shaughnessy Rd, Langford Gardens, Bengaluru, Karnataka 560025, India; (M.A.I.); (V.P.S.R.); (S.M.); (S.S.); (D.B.D.)
| | | | - Dawood Babu Dudekula
- 3BIGS Omicscore Pvt. Ltd., 1, O Shaughnessy Rd, Langford Gardens, Bengaluru, Karnataka 560025, India; (M.A.I.); (V.P.S.R.); (S.M.); (S.S.); (D.B.D.)
| | - Junhyung Park
- 3BIGS Co., Ltd., 156, Gwanggyo-ro, Yeongtong-gu, Suwon-si 16506, Korea;
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20
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Aparicio-Prat E, Yan D, Mariotti M, Bassik M, Hess G, Fortin JP, Weston A, Xi HS, Stanton R. Roadmap for the use of base editors to decipher drug mechanism of action. PLoS One 2021; 16:e0257537. [PMID: 34547052 PMCID: PMC8454938 DOI: 10.1371/journal.pone.0257537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 09/05/2021] [Indexed: 11/19/2022] Open
Abstract
CRISPR base editors are powerful tools for large-scale mutagenesis studies. This kind of approach can elucidate the mechanism of action of compounds, a key process in drug discovery. Here, we explore the utility of base editors in an early drug discovery context focusing on G-protein coupled receptors. A pooled mutagenesis screening framework was set up based on a modified version of the CRISPR-X base editor system. We determine optimized experimental conditions for mutagenesis where sgRNAs are delivered by cell transfection or viral infection over extended time periods (>14 days), resulting in high mutagenesis produced in a short region located at -4/+8 nucleotides with respect to the sgRNA match. The β2 Adrenergic Receptor (B2AR) was targeted in this way employing a 6xCRE-mCherry reporter system to monitor its response to isoproterenol. The results of our screening indicate that residue 184 of B2AR is crucial for its activation. Based on our experience, we outline the crucial points to consider when designing and performing CRISPR-based pooled mutagenesis screening, including the typical technical hurdles encountered when studying compound pharmacology.
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MESH Headings
- CRISPR-Cas Systems/genetics
- Gene Editing/methods
- Genes, Reporter
- HEK293 Cells
- Humans
- Isoproterenol/chemistry
- Isoproterenol/metabolism
- Luminescent Proteins/genetics
- Luminescent Proteins/metabolism
- Mutagenesis, Site-Directed
- RNA Interference
- RNA, Guide, CRISPR-Cas Systems/metabolism
- RNA, Small Interfering/metabolism
- Receptors, Adrenergic, beta-2/chemistry
- Receptors, Adrenergic, beta-2/genetics
- Receptors, Adrenergic, beta-2/metabolism
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Affiliation(s)
- Estel Aparicio-Prat
- Simulation and Modelling Sciences, Pfizer, Cambridge, Massachusetts, United States of America
| | - Dong Yan
- Internal Medicine Research Unit, Pfizer, Cambridge, Massachusetts, United States of America
| | - Marco Mariotti
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Facultat de Biologia, Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Michael Bassik
- Department of Genetics, Stanford University, Palo Alto, California, United States of America
| | - Gaelen Hess
- Department of Genetics, Stanford University, Palo Alto, California, United States of America
| | - Jean-Philippe Fortin
- Internal Medicine Research Unit, Pfizer, Cambridge, Massachusetts, United States of America
| | - Andrea Weston
- Discovery Sciences, Pfizer, Groton, Connecticut, United States of America
| | - Hualin S. Xi
- Simulation and Modelling Sciences, Pfizer, Cambridge, Massachusetts, United States of America
| | - Robert Stanton
- Simulation and Modelling Sciences, Pfizer, Cambridge, Massachusetts, United States of America
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21
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Singh K, Nassar N, Bachari A, Schanknecht E, Telukutla S, Zomer R, Piva TJ, Mantri N. The Pathophysiology and the Therapeutic Potential of Cannabinoids in Prostate Cancer. Cancers (Basel) 2021; 13:4107. [PMID: 34439262 PMCID: PMC8392233 DOI: 10.3390/cancers13164107] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 08/13/2021] [Accepted: 08/13/2021] [Indexed: 12/19/2022] Open
Abstract
Prostate cancer is the second most frequently occurring cancer diagnosed among males. Recent preclinical evidence implicates cannabinoids as powerful regulators of cell growth and differentiation. In this review, we focused on studies that demonstrated anticancer effects of cannabinoids and their possible mechanisms of action in prostate cancer. Besides the palliative effects of cannabinoids, research from the past two decades has demonstrated their promising potential as antitumor agents in a wide variety of cancers. This analysis may provide pharmacological insights into the selection of specific cannabinoids for the development of antitumor drugs for the treatment of prostate cancer.
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Affiliation(s)
- Kanika Singh
- The Pangenomics Lab, School of Science, RMIT University, Bundoora, VIC 3083, Australia; (K.S.); (A.B.); (E.S.); (S.T.)
| | - Nazim Nassar
- School of Health and Biomedical Sciences, RMIT University, Bundoora, VIC 3083, Australia; (N.N.); (T.J.P.)
| | - Ava Bachari
- The Pangenomics Lab, School of Science, RMIT University, Bundoora, VIC 3083, Australia; (K.S.); (A.B.); (E.S.); (S.T.)
| | - Ellen Schanknecht
- The Pangenomics Lab, School of Science, RMIT University, Bundoora, VIC 3083, Australia; (K.S.); (A.B.); (E.S.); (S.T.)
| | - Srinivasareddy Telukutla
- The Pangenomics Lab, School of Science, RMIT University, Bundoora, VIC 3083, Australia; (K.S.); (A.B.); (E.S.); (S.T.)
| | - Roby Zomer
- MGC Pharmaceuticals Limited, West Perth, WA 6005, Australia;
| | - Terrence J. Piva
- School of Health and Biomedical Sciences, RMIT University, Bundoora, VIC 3083, Australia; (N.N.); (T.J.P.)
| | - Nitin Mantri
- The Pangenomics Lab, School of Science, RMIT University, Bundoora, VIC 3083, Australia; (K.S.); (A.B.); (E.S.); (S.T.)
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009, Australia
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22
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Amini H, Rezabakhsh A, Heidarzadeh M, Hassanpour M, Hashemzadeh S, Ghaderi S, Sokullu E, Rahbarghazi R, Reiter RJ. An Examination of the Putative Role of Melatonin in Exosome Biogenesis. Front Cell Dev Biol 2021; 9:686551. [PMID: 34169078 PMCID: PMC8219171 DOI: 10.3389/fcell.2021.686551] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 05/07/2021] [Indexed: 12/16/2022] Open
Abstract
During the last two decades, melatonin has been found to have pleiotropic effects via different mechanisms on its target cells. Data are abundant for some aspects of the signaling pathways within cells while other casual mechanisms have not been adequately addressed. From an evolutionary perspective, eukaryotic cells are equipped with a set of interrelated endomembrane systems consisting of intracellular organelles and secretory vesicles. Of these, exosomes are touted as cargo-laden secretory vesicles that originate from the endosomal multivesicular machinery which participate in a mutual cross-talk at different cellular interfaces. It has been documented that cells transfer various biomolecules and genetic elements through exosomes to sites remote from the original cell in a paracrine manner. Findings related to the molecular mechanisms between melatonin and exosomal biogenesis and cargo sorting are the subject of the current review. The clarification of the interplay between melatonin and exosome biogenesis and cargo sorting at the molecular level will help to define a cell's secretion capacity. This review precisely addresses the role and potential significance of melatonin in determining the efflux capacity of cells via the exosomal pathway. Certain cells, for example, stem cells actively increase exosome efflux in response to melatonin treatment which accelerates tissue regeneration after transplantation into the injured sites.
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Affiliation(s)
- Hassan Amini
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Aysa Rezabakhsh
- Cardiovascular Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Morteza Heidarzadeh
- Koç University Translational Medicine Research Center (KUTTAM), Istanbul, Turkey
| | - Mehdi Hassanpour
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Shahriar Hashemzadeh
- Tuberculosis and Lung Disease Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Shahrouz Ghaderi
- Medical Faculty, Institute of Molecular Medicine III, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Emel Sokullu
- Koç University Translational Medicine Research Center (KUTTAM), Istanbul, Turkey
| | - Reza Rahbarghazi
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Applied Cell Sciences, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Russel J Reiter
- Department of Cell Systems and Anatomy, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
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23
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Yang Z, Xu H, Wang J, Chen W, Zhao M. Single-Molecule Fluorescence Techniques for Membrane Protein Dynamics Analysis. APPLIED SPECTROSCOPY 2021; 75:491-505. [PMID: 33825543 DOI: 10.1177/00037028211009973] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Fluorescence-based single-molecule techniques, mainly including fluorescence correlation spectroscopy (FCS) and single-molecule fluorescence resonance energy transfer (smFRET), are able to analyze the conformational dynamics and diversity of biological macromolecules. They have been applied to analysis of the dynamics of membrane proteins, such as membrane receptors and membrane transport proteins, due to their superior ability in resolving spatio-temporal heterogeneity and the demand of trace amounts of analytes. In this review, we first introduced the basic principle involved in FCS and smFRET. Then we summarized the labeling and immobilization strategies of membrane protein molecules, the confocal-based and TIRF-based instrumental configuration, and the data processing methods. The applications to membrane protein dynamics analysis are described in detail with the focus on how to select suitable fluorophores, labeling sites, experimental setup, and analysis methods. In the last part, the remaining challenges to be addressed and further development in this field are also briefly discussed.
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Affiliation(s)
- Ziyu Yang
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, 12465 Peking University, Beijing, China
| | - Haiqi Xu
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, 12465 Peking University, Beijing, China
| | - Jiayu Wang
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, 12465 Peking University, Beijing, China
| | - Wei Chen
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, 12465 Peking University, Beijing, China
| | - Meiping Zhao
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, 12465 Peking University, Beijing, China
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24
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Targeting protein self-association in drug design. Drug Discov Today 2021; 26:1148-1163. [PMID: 33548462 DOI: 10.1016/j.drudis.2021.01.028] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/24/2020] [Accepted: 01/26/2021] [Indexed: 01/05/2023]
Abstract
Protein self-association is a universal phenomenon essential for stability and molecular recognition. Disrupting constitutive homomers constitutes an original and emerging strategy in drug design. Inhibition of homomeric proteins can be achieved through direct complex disruption, subunit intercalation, or by promoting inactive oligomeric states. Targeting self-interaction grants several advantages over active site inhibition because of the stimulation of protein degradation, the enhancement of selectivity, substoichiometric inhibition, and by-pass of compensatory mechanisms. This new landscape in protein inhibition is driven by the development of biophysical and biochemical tools suited for the study of homomeric proteins, such as differential scanning fluorimetry (DSF), native mass spectrometry (MS), Förster resonance energy transfer (FRET) spectroscopy, 2D nuclear magnetic resonance (NMR), and X-ray crystallography. In this review, we discuss the different aspects of this new paradigm in drug design.
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25
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Dekan Z, Kremsmayr T, Keov P, Godin M, Teakle N, Dürrauer L, Xiang H, Gharib D, Bergmayr C, Hellinger R, Gay M, Vilaseca M, Kurzbach D, Albericio F, Alewood PF, Gruber CW, Muttenthaler M. Nature-inspired dimerization as a strategy to modulate neuropeptide pharmacology exemplified with vasopressin and oxytocin. Chem Sci 2021; 12:4057-4062. [PMID: 34163676 PMCID: PMC8179488 DOI: 10.1039/d0sc05501h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Vasopressin (VP) and oxytocin (OT) are cyclic neuropeptides that regulate fundamental physiological functions via four G protein-coupled receptors, V1aR, V1bR, V2R, and OTR. Ligand development remains challenging for these receptors due to complex structure–activity relationships. Here, we investigated dimerization as a strategy for developing ligands with novel pharmacology. We regioselectively synthesised and systematically studied parallel, antiparallel and N- to C-terminal cyclized homo- and heterodimer constructs of VP, OT and dVDAVP (1-deamino-4-valine-8-d-arginine-VP). All disulfide-linked dimers, except for the head-to-tail cyclized constructs, retained nanomolar potency despite the structural implications of dimerization. Our results support a single chain interaction for receptor activation. Dimer orientation had little impact on activity, except for the dVDAVP homodimers, where an antagonist to agonist switch was observed at the V1aR. This study provides novel insights into the structural requirements of VP/OT receptor activation and spotlights dimerization as a strategy to modulate pharmacology, a concept also frequently observed in nature. Structural and pharmacological study of parallel, antiparallel and N- to C-terminal cyclized homo- and heterodimers of vasopressin and oxytocin. This study spotlights dimerization as a strategy to modulate the pharmacology of neuropeptides.![]()
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Affiliation(s)
- Zoltan Dekan
- Institute for Molecular Bioscience, The University of Queensland Brisbane 4072 Australia
| | - Thomas Kremsmayr
- Institute of Biological Chemistry, University of Vienna Währingerstraße 38 1090 Vienna Austria
| | - Peter Keov
- Faculty of Medicine, School of Biomedical Sciences, The University of Queensland Brisbane 4072 Australia
| | - Mathilde Godin
- Institute for Molecular Bioscience, The University of Queensland Brisbane 4072 Australia
| | - Ngari Teakle
- Institute for Molecular Bioscience, The University of Queensland Brisbane 4072 Australia
| | - Leopold Dürrauer
- Institute of Biological Chemistry, University of Vienna Währingerstraße 38 1090 Vienna Austria
| | - Huang Xiang
- Center for Physiology and Pharmacology, Medical University of Vienna Schwarzspanierstraße 17 1090 Vienna Austria
| | - Dalia Gharib
- Center for Physiology and Pharmacology, Medical University of Vienna Schwarzspanierstraße 17 1090 Vienna Austria
| | - Christian Bergmayr
- Center for Physiology and Pharmacology, Medical University of Vienna Schwarzspanierstraße 17 1090 Vienna Austria
| | - Roland Hellinger
- Center for Physiology and Pharmacology, Medical University of Vienna Schwarzspanierstraße 17 1090 Vienna Austria
| | - Marina Gay
- Institute for Research in Biomedicine Barcelona C/ Baldiri Reixac 10 08028 Barcelona Spain
| | - Marta Vilaseca
- Institute for Research in Biomedicine Barcelona C/ Baldiri Reixac 10 08028 Barcelona Spain
| | - Dennis Kurzbach
- Institute of Biological Chemistry, University of Vienna Währingerstraße 38 1090 Vienna Austria
| | - Fernando Albericio
- Department of Organic Chemistry, University of Barcelona Barcelona Science Park, Baldiri Reixac 10 08028 Barcelona Spain
| | - Paul F Alewood
- Institute for Molecular Bioscience, The University of Queensland Brisbane 4072 Australia
| | - Christian W Gruber
- Faculty of Medicine, School of Biomedical Sciences, The University of Queensland Brisbane 4072 Australia.,Center for Physiology and Pharmacology, Medical University of Vienna Schwarzspanierstraße 17 1090 Vienna Austria
| | - Markus Muttenthaler
- Institute for Molecular Bioscience, The University of Queensland Brisbane 4072 Australia .,Institute of Biological Chemistry, University of Vienna Währingerstraße 38 1090 Vienna Austria
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26
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Xu D, Xie L, Zhang Z, Wang D, Qiu J, Yu W, Xu C, He C, Xu X, Yin J. Preliminary Investigation about the Expression of G Protein-Coupled Receptors in Platelets from Patients with Chronic Immune Thrombocytopenic Purpura. Acta Haematol 2021; 144:551-559. [PMID: 33849009 DOI: 10.1159/000514907] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 02/02/2021] [Indexed: 02/05/2023]
Abstract
OBJECTIVE The objective of this study was to determine the expression of G protein-coupled receptors (GPCRs) in platelets from adult patients with chronic immune thrombocytopenic purpura (ITP). METHODS Peripheral blood samples were collected from 40 patients with chronic ITP in the Second Affiliated Hospital of Shantou University Medical College, and 40 peripheral blood samples from healthy volunteers were collected; expressions of the adenosine diphosphate receptors (P2Y1 and P2Y12), alpha-2A adrenergic receptor (α2A-AR), and thromboxane A2 receptor (TP) in platelets were detected by flow cytometry. Gα protein, protease-activated receptor 1 (PAR1), and protease-activated receptor 4 (PAR4) were analyzed by Western blot and analyzed statistically. RESULTS Flow cytometry measurements of mean fluorescence intensities showed platelets from patients with chronic ITP, compared to healthy individuals, had significantly higher levels of P2Y1 (31.4 ± 2.2 vs. 7.8 ± 0.8), P2Y12 (29.6 ± 2.1 vs. 7.2 ± 1.3), α2A-AR (25.8 ± 2.9 vs. 9.8 ± 0.9), and TP (39.8 ± 3.1 vs. 4.7 ± 0.6) (all p < 0.01). Similarly, integrated optical density analysis of Western blots showed that platelets from patients with chronic ITP had significantly higher levels of Gα (1046.3 ± 159.96 vs. 254.49 ± 39.51), PAR1 (832.98 ± 98.81 vs. 203.92 ± 27.47), and PAR4 (1518.80 ± 272.45 vs. 431.27 ± 41.86) (all p < 0.01). CONCLUSION Expression of GPCRs is increased in platelets from patients with chronic ITP, suggesting that platelets of chronic ITP may participate in the complicated biological process by means of GPCR-mediated signaling pathways.
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Affiliation(s)
- Daming Xu
- Division of Urological Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Long Xie
- Department of Clinical Laboratory Medicine, The Second Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Zewen Zhang
- Division of Hematology, The Second Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Duanxu Wang
- Office of Medical Affairs Administration, The Second Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Jinfeng Qiu
- Division of Respirology, The Second Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Wenjun Yu
- Division of Hematology, The Second Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Chengwei Xu
- Department of Hemodialysis, The Second Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Chunling He
- Department of Pathology, The Second Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Xianru Xu
- Division of Inventional Ultrasonic Therapeutics, The Second Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Jun Yin
- Department of Clinical Laboratory Medicine, The Second Affiliated Hospital of Shantou University Medical College, Shantou, China
- Division of Hematology, The Second Affiliated Hospital of Shantou University Medical College, Shantou, China
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27
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G proteins: binary switches in health and disease. Cent Eur J Immunol 2020; 45:364-367. [PMID: 33437192 PMCID: PMC7789995 DOI: 10.5114/ceji.2020.101271] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Accepted: 04/29/2018] [Indexed: 12/18/2022] Open
Abstract
Cell signaling plays critical role in health and disease. The normal functioning of body depends on the homeostasis of immunity players. One of the very important cell signaling participants is G protein-coupled receptor (GPCR). GPCRs transduce extracellular signals into target cell by binding to and activating different G proteins (G αβγ, families Gi, Gs, Gq/11, G12/13) leading to range of different functions. Abnormal GPCRs signaling leads to various abnormalities, including but not limited to, cancer, pain, cardiac problems, and asthma. Mutations, which lead to activation or inactivation of GPCR pathways, permanently alter the pathways controlled by these receptors. A large number of human cancer incidence is a consequence of genetic abnormalities in signaling pathways, which influence cell division. Some bacteria and pathogens may interfere with the GPCR signaling pathways for their survival and immune evasion. Inhibition of GPCR signaling by small inhibitors is a novel way to treat various pathological conditions. There are several types of GPCRs in human genome, which due to their central role in health and disease, are the target of many commercially available drugs. Importantly, GPCRs have huge impact on drug discovery and approximately 30% of current drug targets are GPCRs. There is a need of further studies to explore more the role of G protein and the GPCRs in human health and how certain mutations can lead to disease state. Such studies may be important to adjust the signaling pathways for health improvement.
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28
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Sarfaraz S, Muneer I, Liu H. Combining fragment docking with graph theory to improve ligand docking for homology model structures. J Comput Aided Mol Des 2020; 34:1237-1259. [PMID: 33034007 PMCID: PMC7544562 DOI: 10.1007/s10822-020-00345-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 09/24/2020] [Indexed: 11/30/2022]
Abstract
Computational protein–ligand docking is well-known to be prone to inaccuracies in input receptor structures, and it is challenging to obtain good docking results with computationally predicted receptor structures (e.g. through homology modeling). Here we introduce a fragment-based docking method and test if it reduces requirements on the accuracy of an input receptor structures relative to non-fragment docking approaches. In this method, small rigid fragments are docked first using AutoDock Vina to generate a large number of favorably docked poses spanning the receptor binding pocket. Then a graph theory maximum clique algorithm is applied to find combined sets of docked poses of different fragment types onto which the complete ligand can be properly aligned. On the basis of these alignments, possible binding poses of complete ligand are determined. This docking method is first tested for bound docking on a series of Cytochrome P450 (CYP450) enzyme–substrate complexes, in which experimentally determined receptor structures are used. For all complexes tested, ligand poses of less than 1 Å root mean square deviations (RMSD) from the actual binding positions can be recovered. Then the method is tested for unbound docking with modeled receptor structures for a number of protein–ligand complexes from different families including the very recent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) protease. For all complexes, poses with RMSD less than 3 Å from actual binding positions can be recovered. Our results suggest that for docking with approximately modeled receptor structures, fragment-based methods can be more effective than common complete ligand docking approaches.
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Affiliation(s)
- Sara Sarfaraz
- School of life sciences, University of Science and Technology of China, Hefei, 230026, Anhui, China
| | - Iqra Muneer
- School of life sciences, University of Science and Technology of China, Hefei, 230026, Anhui, China
| | - Haiyan Liu
- School of life sciences, University of Science and Technology of China, Hefei, 230026, Anhui, China.
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29
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Yang Z, Liang XF, Li GL, Tao YX. Biased signaling in fish melanocortin-4 receptors (MC4Rs): Divergent pharmacology of four ligands on spotted scat (Scatophagus argus) and grass carp (Ctenopharyngodon idella) MC4Rs. Mol Cell Endocrinol 2020; 515:110929. [PMID: 32615281 DOI: 10.1016/j.mce.2020.110929] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/19/2020] [Accepted: 06/24/2020] [Indexed: 12/24/2022]
Abstract
The melanocortin-4 receptor (MC4R) plays a critical role in the regulation of energy homeostasis in both mammals and fish. Several fish MC4Rs recently characterized have high constitutive activities, potentially associated with food intake and growth rate. In the present study, we systematically investigated the effects of four human MC4R (hMC4R) antagonists, including agouti-related peptide (AgRP), Ipsen 5i, ML00253764, and MCL0020, on the cAMP and ERK1/2 signaling of two fish MC4Rs: spotted scat (Scatophagus argus) MC4R (saMC4R) and grass carp (Ctenopharyngodon idella) MC4R (ciMC4R), with hMC4R as a control. We showed that both saMC4R and ciMC4R were constitutively active with significantly increased basal cAMP levels. AgRP acted as an inverse agonist in cAMP signaling pathway in both fish MC4Rs whereas MCL0020 functioned as an inverse agonist for ciMC4R but a weak neutral antagonist for saMC4R. Ipsen 5i and MCL0020 behaved as neutral allosteric modulators in the cAMP signaling of fish MC4Rs. The saMC4R and ciMC4R had similar basal pERK1/2 levels as hMC4R and the pERK1/2 levels of the two fish MC4Rs were significantly increased upon stimulation with all four ligands. In summary, our studies demonstrated the existence of biased signaling in fish MC4R. We also showed dramatic pharmacological differences of human and fish MC4Rs with synthetic ligands. Our data provided novel insights and led to a better understanding of fish MC4R pharmacology.
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Affiliation(s)
- Zhao Yang
- Department of Anatomy, Physiology and Pharmacology, College of Veterinary Medicine, Auburn University, Auburn, AL, 36849, United States
| | - Xu-Fang Liang
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Hubei Collaborative Innovation Center for Freshwater Aquaculture, Wuhan, Hubei, 430070, China
| | - Guang-Li Li
- Fisheries College, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Ya-Xiong Tao
- Department of Anatomy, Physiology and Pharmacology, College of Veterinary Medicine, Auburn University, Auburn, AL, 36849, United States.
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30
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Gong J, Chen Y, Pu F, Sun P, He F, Zhang L, Li Y, Ma Z, Wang H. Understanding Membrane Protein Drug Targets in Computational Perspective. Curr Drug Targets 2020; 20:551-564. [PMID: 30516106 DOI: 10.2174/1389450120666181204164721] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 09/03/2018] [Accepted: 09/04/2018] [Indexed: 01/16/2023]
Abstract
Membrane proteins play crucial physiological roles in vivo and are the major category of drug targets for pharmaceuticals. The research on membrane protein is a significant part in the drug discovery. The biological process is a cycled network, and the membrane protein is a vital hub in the network since most drugs achieve the therapeutic effect via interacting with the membrane protein. In this review, typical membrane protein targets are described, including GPCRs, transporters and ion channels. Also, we conclude network servers and databases that are referring to the drug, drug-target information and their relevant data. Furthermore, we chiefly introduce the development and practice of modern medicines, particularly demonstrating a series of state-of-the-art computational models for the prediction of drug-target interaction containing network-based approach and machine-learningbased approach as well as showing current achievements. Finally, we discuss the prospective orientation of drug repurposing and drug discovery as well as propose some improved framework in bioactivity data, created or improved predicted approaches, alternative understanding approaches of drugs bioactivity and their biological processes.
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Affiliation(s)
- Jianting Gong
- School of Information Science and Technology, Northeast Normal University, Changchun, China.,Institution of Computational Biology, Northeast Normal University, Changchun, China
| | - Yongbing Chen
- School of Information Science and Technology, Northeast Normal University, Changchun, China.,Institution of Computational Biology, Northeast Normal University, Changchun, China
| | - Feng Pu
- School of Information Science and Technology, Northeast Normal University, Changchun, China.,Institution of Computational Biology, Northeast Normal University, Changchun, China
| | - Pingping Sun
- School of Information Science and Technology, Northeast Normal University, Changchun, China.,Institution of Computational Biology, Northeast Normal University, Changchun, China
| | - Fei He
- School of Information Science and Technology, Northeast Normal University, Changchun, China.,Institution of Computational Biology, Northeast Normal University, Changchun, China
| | - Li Zhang
- School of Computer Science and Engineering, Changchun University of Technology, Changchun, China
| | - Yanwen Li
- School of Information Science and Technology, Northeast Normal University, Changchun, China.,Institution of Computational Biology, Northeast Normal University, Changchun, China
| | - Zhiqiang Ma
- School of Information Science and Technology, Northeast Normal University, Changchun, China.,Institution of Computational Biology, Northeast Normal University, Changchun, China
| | - Han Wang
- School of Information Science and Technology, Northeast Normal University, Changchun, China.,Institution of Computational Biology, Northeast Normal University, Changchun, China
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31
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Scharf MM, Zimmermann M, Wilhelm F, Stroe R, Waldhoer M, Kolb P. A Focus on Unusual ECL2 Interactions Yields β 2 -Adrenergic Receptor Antagonists with Unprecedented Scaffolds. ChemMedChem 2020; 15:882-890. [PMID: 32301583 PMCID: PMC7318225 DOI: 10.1002/cmdc.201900715] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 03/11/2020] [Indexed: 11/15/2022]
Abstract
The binding pockets of aminergic G protein-coupled receptors are often targeted by drugs and virtual screening campaigns. In order to find ligands with unprecedented scaffolds for one of the best-investigated receptors of this subfamily, the β2 -adrenergic receptor, we conducted a docking-based screen insisting that molecules would address previously untargeted residues in extracellular loop 2. We here report the discovery of ligands with a previously undescribed coumaran-based scaffold. Furthermore, we provide an analysis of the added value that X-ray structures in different conformations deliver for such docking screens.
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Affiliation(s)
- Magdalena M. Scharf
- Department of Pharmaceutical ChemistryPhilipps-University MarburgMarbacher Weg 635037MarburgGermany
| | | | - Florian Wilhelm
- InterAx BiotechPARK innovAARE5234VilligenSwitzerland
- Department of Biosystems Science and Engineering ETHETH ZürichMattenstrasse 264058BaselSwitzerland
| | - Raimond Stroe
- InterAx BiotechPARK innovAARE5234VilligenSwitzerland
- Department of Drug Design and PharmacologyUniversity of CopenhagenUniversitetsparken 22100CopenhagenDenmark
| | | | - Peter Kolb
- Department of Pharmaceutical ChemistryPhilipps-University MarburgMarbacher Weg 635037MarburgGermany
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32
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Abstract
Today, excluding insulin, there are eight classes of anti-diabetic medicines that have been added to the pharmacy since the introduction of metformin in the mid-1950s; the sulfonylureas, biguanides, thiazolidinediones, α-glucosidase inhibitors, meglitinides, incretins, and sodium glucose transport 2 inhibitors. Does the fact that metformin is still first-line treatment suggest that our drug discovery efforts over the past 60 years have not been good enough? Or does it suggest that diabetes is such a complex disorder that no single treatment, other than gastric bypass surgery, can affect true normalization of not only blood sugar but also the underlying pathologies? Our understanding of the disease has most definitely improved which may bring hope for the future in terms of science, but for it to be beneficial, this science has to be translated into better drug treatments for the disease. In this review, I have examined the eight classes of anti-diabetes drugs from a drug discovery perspective.
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Affiliation(s)
- John C Clapham
- Medical School, University of Buckingham, Buckingham, UK.
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33
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Jung O, Beauvais DM, Adams KM, Rapraeger AC. VLA-4 phosphorylation during tumor and immune cell migration relies on its coupling to VEGFR2 and CXCR4 by syndecan-1. J Cell Sci 2019; 132:jcs.232645. [PMID: 31562188 DOI: 10.1242/jcs.232645] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 09/20/2019] [Indexed: 12/19/2022] Open
Abstract
When targeted by the tumor-promoting enzyme heparanase, cleaved and shed syndecan-1 (Sdc1) then couples VEGFR2 (also known as KDR) to VLA-4, activating VEGFR2 and the directed migration of myeloma cells. But how VEGFR2 activates VLA-4-mediated motility has remained unknown. We now report that VEGFR2 causes PKA-mediated phosphorylation of VLA-4 on S988, an event known to stimulate tumor metastasis while suppressing cytotoxic immune cells. A key partner in this mechanism is the chemokine receptor CXCR4, a well-known mediator of cell motility in response to gradients of the chemokine SDF-1 (also known as CXCL12). The entire machinery necessary to phosphorylate VLA-4, consisting of CXCR4, AC7 (also known as ADCY7) and PKA, is constitutively associated with VEGFR2 and is localized to the integrin by Sdc1. VEGFR2 carries out the novel phosphorylation of Y135 within the DRY microswitch of CXCR4, sequentially activating Gαiβγ, AC7 and PKA, which phosphorylates S988 on the integrin. This mechanism is blocked by a syndecan-mimetic peptide (SSTNVEGFR2), which, by preventing VEGFR2 linkage to VLA-4, arrests tumor cell migration that depends on VLA-4 phosphorylation and stimulates the LFA-1-mediated migration of cytotoxic leukocytes.
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Affiliation(s)
- Oisun Jung
- Department of Human Oncology, School of Medicine and Public Health, University of Wisconsin-Madison, 1111 Highland Avenue, Madison, WI 53705, USA.,Graduate Program in Molecular and Cellular Pharmacology, School of Medicine and Public Health, University of Wisconsin-Madison, 1111 Highland Avenue, Madison, WI 53705, USA
| | - DeannaLee M Beauvais
- Department of Human Oncology, School of Medicine and Public Health, University of Wisconsin-Madison, 1111 Highland Avenue, Madison, WI 53705, USA
| | - Kristin M Adams
- Department of Human Oncology, School of Medicine and Public Health, University of Wisconsin-Madison, 1111 Highland Avenue, Madison, WI 53705, USA
| | - Alan C Rapraeger
- Department of Human Oncology, School of Medicine and Public Health, University of Wisconsin-Madison, 1111 Highland Avenue, Madison, WI 53705, USA .,Graduate Program in Molecular and Cellular Pharmacology, School of Medicine and Public Health, University of Wisconsin-Madison, 1111 Highland Avenue, Madison, WI 53705, USA
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34
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M3 muscarinic receptor activation reduces hepatocyte lipid accumulation via CaMKKβ/AMPK pathway. Biochem Pharmacol 2019; 169:113613. [PMID: 31445019 DOI: 10.1016/j.bcp.2019.08.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 08/19/2019] [Indexed: 12/21/2022]
Abstract
Previously, we reported that hepatic muscarinic receptors modulate both acute and chronic liver injury, however, the role of muscarinic receptors in fatty liver disease is unclear. We observed in patients who underwent weight loss surgery, a decrease in hepatic expression of M3 muscarinic receptors (M3R). We also observed that fat loading of hepatocytes, increased M3R expression. Based on these observations, we tested the hypothesis that M3R regulate hepatocyte lipid accumulation. Incubation of AML12 hepatocytes with 1 mM oleic acid resulted in lipid accumulation that was significantly reduced by co-treatment with a muscarinic agonist (pilocarpine or carbachol), an effect blocked by atropine (a muscarinic antagonist). Similar treatment of Hepa 1-6 cells, a mouse hepatoblastoma cell line, showed comparable results. In both, control and fat-loaded AML12 cells, pilocarpine induced time-dependent AMPKα phosphorylation and significantly up-regulated lipolytic genes (ACOX1, CPT1, and PPARα). Compound C, a selective and reversible AMPK inhibitor, significantly blunted pilocarpine-mediated reduction of lipid accumulation and pilocarpine-mediated up-regulation of lipolytic genes. BAPTA-AM, a calcium chelator, and STO-609, a calcium/calmodulin-dependent protein kinase kinase inhibitor, attenuated agonist-induced AMPKα phosphorylation. Finally, M3R siRNA attenuated agonist-induced AMPKα phosphorylation as well as agonist-mediated reduction of hepatocyte steatosis. In conclusion, this proof-of-concept study demonstrates that M3R has protective effects against hepatocyte lipid accumulation by activating AMPK pathway and is a potential therapeutic target for non-alcoholic fatty liver disease.
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35
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Zhao DY, Pöge M, Morizumi T, Gulati S, Van Eps N, Zhang J, Miszta P, Filipek S, Mahamid J, Plitzko JM, Baumeister W, Ernst OP, Palczewski K. Cryo-EM structure of the native rhodopsin dimer in nanodiscs. J Biol Chem 2019; 294:14215-14230. [PMID: 31399513 DOI: 10.1074/jbc.ra119.010089] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Revised: 08/02/2019] [Indexed: 02/03/2023] Open
Abstract
Imaging of rod photoreceptor outer-segment disc membranes by atomic force microscopy and cryo-electron tomography has revealed that the visual pigment rhodopsin, a prototypical class A G protein-coupled receptor (GPCR), can organize as rows of dimers. GPCR dimerization and oligomerization offer possibilities for allosteric regulation of GPCR activity, but the detailed structures and mechanism remain elusive. In this investigation, we made use of the high rhodopsin density in the native disc membranes and of a bifunctional cross-linker that preserves the native rhodopsin arrangement by covalently tethering rhodopsins via Lys residue side chains. We purified cross-linked rhodopsin dimers and reconstituted them into nanodiscs for cryo-EM analysis. We present cryo-EM structures of the cross-linked rhodopsin dimer as well as a rhodopsin dimer reconstituted into nanodiscs from purified monomers. We demonstrate the presence of a preferential 2-fold symmetrical dimerization interface mediated by transmembrane helix 1 and the cytoplasmic helix 8 of rhodopsin. We confirmed this dimer interface by double electron-electron resonance measurements of spin-labeled rhodopsin. We propose that this interface and the arrangement of two protomers is a prerequisite for the formation of the observed rows of dimers. We anticipate that the approach outlined here could be extended to other GPCRs or membrane receptors to better understand specific receptor dimerization mechanisms.
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Affiliation(s)
- Dorothy Yanling Zhao
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Matthias Pöge
- Department of Molecular Structural Biology, Max-Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Takefumi Morizumi
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Sahil Gulati
- Gavin Herbert Eye Institute and the Department of Ophthalmology, University of California, Irvine, California 92697.,Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio 44106
| | - Ned Van Eps
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Jianye Zhang
- Gavin Herbert Eye Institute and the Department of Ophthalmology, University of California, Irvine, California 92697.,Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio 44106
| | - Przemyslaw Miszta
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw 02-093, Poland
| | - Slawomir Filipek
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw 02-093, Poland
| | - Julia Mahamid
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Jürgen M Plitzko
- Department of Molecular Structural Biology, Max-Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Wolfgang Baumeister
- Department of Molecular Structural Biology, Max-Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Oliver P Ernst
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada .,Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Krzysztof Palczewski
- Gavin Herbert Eye Institute and the Department of Ophthalmology, University of California, Irvine, California 92697 .,Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio 44106
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Getter T, Gulati S, Zimmerman R, Chen Y, Vinberg F, Palczewski K. Stereospecific modulation of dimeric rhodopsin. FASEB J 2019; 33:9526-9539. [PMID: 31121099 PMCID: PMC6662988 DOI: 10.1096/fj.201900443rr] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 04/23/2019] [Indexed: 11/11/2022]
Abstract
The classic concept that GPCRs function as monomers has been challenged by the emerging evidence of GPCR dimerization and oligomerization. Rhodopsin (Rh) is the only GPCR whose native oligomeric arrangement was revealed by atomic force microscopy demonstrating that Rh exists as a dimer. However, the role of Rh dimerization in retinal physiology is currently unknown. In this study, we identified econazole and sulconazole, two small molecules that disrupt Rh dimer contacts, by implementing a cell-based high-throughput screening assay. Racemic mixtures of identified lead compounds were separated and tested for their stereospecific binding to Rh using UV-visible spectroscopy and intrinsic fluorescence of tryptophan (Trp) 265 after illumination. By following the changes in UV-visible spectra and Trp265 fluorescence in vitro, we found that binding of R-econazole modulates the formation of Meta III and quenches the intrinsic fluorescence of Trp265. In addition, electrophysiological ex vivo recording revealed that R-econazole slows photoresponse kinetics, whereas S-econazole decreased the sensitivity of rods without effecting the kinetics. Thus, this study contributes new methodology to identify compounds that disrupt the dimerization of GPCRs in general and validates the first active compounds that disrupt the Rh dimer specifically.-Getter, T., Gulati, S., Zimmerman, R., Chen, Y., Vinberg, F., Palczewski, K. Stereospecific modulation of dimeric rhodopsin.
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Affiliation(s)
- Tamar Getter
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California–Irvine, California, USA
- Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio, USA
| | - Sahil Gulati
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California–Irvine, California, USA
- Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio, USA
- Department of Physiology and Biophysics, University of California–Irvine, Irvine, California, USA
| | - Remy Zimmerman
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California–Irvine, California, USA
| | - Yuanyuan Chen
- Department of Ophthalmology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- McGowan Institute of Regenerative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Frans Vinberg
- Department of Ophthalmology and Visual Sciences, University of Utah, Salt Lake City, Utah, USA
| | - Krzysztof Palczewski
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California–Irvine, California, USA
- Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio, USA
- Department of Physiology and Biophysics, University of California–Irvine, Irvine, California, USA
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He P, Zhou W, Liu M, Chen Y. Recent Advances of Small Molecular Regulators Targeting G Protein- Coupled Receptors Family for Oncology Immunotherapy. Curr Top Med Chem 2019; 19:1464-1483. [PMID: 31264549 DOI: 10.2174/1568026619666190628115644] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 12/18/2018] [Accepted: 01/02/2019] [Indexed: 12/21/2022]
Abstract
The great clinical success of chimeric antigen receptor T cell (CAR-T) and PD-1/PDL-1 inhibitor therapies suggests the drawing of a cancer immunotherapy age. However, a considerable proportion of cancer patients currently receive little benefit from these treatment modalities, indicating that multiple immunosuppressive mechanisms exist in the tumor microenvironment. In this review, we mainly discuss recent advances in small molecular regulators targeting G Protein-Coupled Receptors (GPCRs) that are associated with oncology immunomodulation, including chemokine receptors, purinergic receptors, prostaglandin E receptor EP4 and opioid receptors. Moreover, we outline how they affect tumor immunity and neoplasia by regulating immune cell recruitment and modulating tumor stromal cell biology. We also summarize the data from recent clinical advances in small molecular regulators targeting these GPCRs, in combination with immune checkpoints blockers, such as PD-1/PDL-1 and CTLA4 inhibitors, for cancer treatments.
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Affiliation(s)
- Peng He
- Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Wenbo Zhou
- Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Mingyao Liu
- Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Yihua Chen
- Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
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Penkauskas T, Preta G. Biological applications of tethered bilayer lipid membranes. Biochimie 2019; 157:131-141. [DOI: 10.1016/j.biochi.2018.11.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 11/19/2018] [Indexed: 12/16/2022]
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Singh KD, Unal H, Desnoyer R, Karnik SS. Mechanism of Hormone Peptide Activation of a GPCR: Angiotensin II Activated State of AT 1R Initiated by van der Waals Attraction. J Chem Inf Model 2019; 59:373-385. [PMID: 30608150 DOI: 10.1021/acs.jcim.8b00583] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
We present a succession of structural changes involved in hormone peptide activation of a prototypical GPCR. Microsecond molecular dynamics simulation generated conformational ensembles reveal propagation of structural changes through key "microswitches" within human AT1R bound to native hormone. The endocrine octa-peptide angiotensin II (AngII) activates AT1R signaling in our bodies which maintains physiological blood pressure, electrolyte balance, and cardiovascular homeostasis. Excessive AT1R activation is associated with pathogenesis of hypertension and cardiovascular diseases which are treated by sartan drugs. The mechanism of AT1R inhibition by sartans has been elucidated by 2.8 Å X-ray structures, mutagenesis, and computational analyses. Yet, the mechanism of AT1R activation by AngII is unclear. The current study delineates an activation scheme initiated by AngII binding. A van der Waals "grasp" interaction between Phe8AngII with Ile2887.39 in AT1R induced mechanical strain pulling Tyr2927.43 and breakage of critical interhelical H-bonds, first between Tyr2927.43 and Val1083.32 and second between Asn1113.35 and Asn2957.46. Subsequently changes are observed in conserved microswitches DRYTM3, Yx7K(R)TM5, CWxPTM6, and NPxxYTM7 in AT1R. Activating the microswitches in the intracellular region of AT1R may trigger formation of the G-protein binding pocket as well as exposure of helix-8 to cytoplasm. Thus, the active-like conformation of AT1R is initiated by the van der Waals interaction of Phe8AngII with Ile2887.39, followed by systematic reorganization of critical interhelical H-bonds and activation of microswitches.
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Affiliation(s)
- Khuraijam Dhanachandra Singh
- Department of Molecular Cardiology, Lerner Research Institute , Cleveland Clinic Foundation , Cleveland , Ohio 44195 , United States
| | - Hamiyet Unal
- Department of Molecular Cardiology, Lerner Research Institute , Cleveland Clinic Foundation , Cleveland , Ohio 44195 , United States
| | - Russell Desnoyer
- Department of Molecular Cardiology, Lerner Research Institute , Cleveland Clinic Foundation , Cleveland , Ohio 44195 , United States
| | - Sadashiva S Karnik
- Department of Molecular Cardiology, Lerner Research Institute , Cleveland Clinic Foundation , Cleveland , Ohio 44195 , United States
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Jardón-Valadez E, Castillo-Guajardo D, Martínez-Luis I, Gutiérrez-Sagal R, Zariñán T, Ulloa-Aguirre A. Molecular dynamics simulation of the follicle-stimulating hormone receptor. Understanding the conformational dynamics of receptor variants at positions N680 and D408 from in silico analysis. PLoS One 2018; 13:e0207526. [PMID: 30462715 PMCID: PMC6248991 DOI: 10.1371/journal.pone.0207526] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 11/01/2018] [Indexed: 11/18/2022] Open
Abstract
Follicle-stimulating hormone receptor (FSHR) is a G-protein coupled receptor (GPCR) and a prototype of the glycoprotein hormone receptors subfamily of GPCRs. Structural data of the FSHR ectodomain in complex with follicle-stimulating hormone suggests a "pull and lift" activation mechanism that triggers a conformational change on the seven α-helix transmembrane domain (TMD). To analyze the conformational changes of the FSHR TMD resulting from sequence variants associated with reproductive impairment in humans, we set up a computational approach combining helix modeling and molecular simulation methods to generate conformational ensembles of the receptor at room (300 K) and physiological (310 K) temperatures. We examined the receptor dynamics in an explicit membrane environment of polyunsaturated phospholipids and solvent water molecules. The analysis of the conformational dynamics of the functional (N680 and S680) and dysfunctional (mutations at D408) variants of the FSHR allowed us to validate the FSHR-TMD model. Functional variants display a concerted motion of flexible intracellular regions at TMD helices 5 and 6. Disruption of side chain interactions and conformational dynamics were detected upon mutation at D408 when replaced with alanine, arginine, or tyrosine. Dynamical network analysis confirmed that TMD helices 2 and 5 may share communication pathways in the functional FSHR variants, whereas no connectivity was detected in the dysfunctional mutants, indicating that the global dynamics of the FSHR was sensitive to mutations at amino acid residue 408, a key position apparently linked to misfolding and variable cell surface plasma membrane expression of FSHRs with distinct mutations at this position.
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Affiliation(s)
- Eduardo Jardón-Valadez
- Departamento de Recursos de la Tierra, Universidad Autónoma Metropolitana, Unidad Lerma, Estado de México, Mexico
| | - Derik Castillo-Guajardo
- Departamento de Ciencias Ambientales Universidad Autónoma Metropolitana, Unidad Lerma, Estado de México, Mexico
| | - Iván Martínez-Luis
- Red de Apoyo a la Investigación, National University of Mexico (UNAM) and Instituto Nacional de Ciencias Médicas y Nutrición SZ, Mexico City, Mexico
| | - Rubén Gutiérrez-Sagal
- Red de Apoyo a la Investigación, National University of Mexico (UNAM) and Instituto Nacional de Ciencias Médicas y Nutrición SZ, Mexico City, Mexico
| | - Teresa Zariñán
- Red de Apoyo a la Investigación, National University of Mexico (UNAM) and Instituto Nacional de Ciencias Médicas y Nutrición SZ, Mexico City, Mexico
| | - Alfredo Ulloa-Aguirre
- Red de Apoyo a la Investigación, National University of Mexico (UNAM) and Instituto Nacional de Ciencias Médicas y Nutrición SZ, Mexico City, Mexico
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Apo-Opsin Exists in Equilibrium Between a Predominant Inactive and a Rare Highly Active State. J Neurosci 2018; 39:212-223. [PMID: 30459230 DOI: 10.1523/jneurosci.1980-18.2018] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 10/30/2018] [Accepted: 11/04/2018] [Indexed: 12/17/2022] Open
Abstract
Bleaching adaptation in rod photoreceptors is mediated by apo-opsin, which activates phototransduction with effective activity 105- to 106-fold lower than that of photoactivated rhodopsin (meta II). However, the mechanism that produces such low opsin activity is unknown. To address this question, we sought to record single opsin responses in mouse rods. We used mutant mice lacking efficient calcium feedback to boosts rod responses and generated a small fraction of opsin by photobleaching ∼1% of rhodopsin. The bleach produced a dramatic increase in the frequency of discrete photoresponse-like events. This activity persisted for hours, was quenched by 11-cis-retinal, and was blocked by uncoupling opsin from phototransduction, all indicating opsin as its source. Opsin-driven discrete activity was also observed in rods containing non-activatable rhodopsin, ruling out transactivation of rhodopsin by opsin. We conclude that bleaching adaptation is mediated by opsin that exists in equilibrium between a predominant inactive and a rare meta II-like state.SIGNIFICANCE STATEMENT Electrophysiological analysis is used to show that the G-protein-coupled receptor opsin exists in equilibrium between a predominant inactive and a rare highly active state that mediates bleaching adaptation in photoreceptors.
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43
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Expanding neuropeptide signalling by multiplying receptor functional states and sub-cellular locations. Cell Tissue Res 2018; 375:49-56. [DOI: 10.1007/s00441-018-2923-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 09/06/2018] [Indexed: 12/13/2022]
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Abstract
Initially G protein-coupled receptors, GPCRs, were thought to act as monomers, but recently strong evidence has been gathered indicating that they are capable of forming homo- and heterodimers or higher order oligomeric complexes, and that the dimerization phenomenon can modulate the pharmacological response and function of these receptors. In this chapter we point to the great potential of alternative therapeutic approach targeted at GPCR dimers, which is especially important in the field of neuropsychopharmacology. We also included a brief description of methods used for studying the phenomenon of GPCR oligomerization, with particular attention paid to the proximity ligation assay, PLA, the procedure which allows the study of interactions between receptors not only in vitro but also in vivo, with good anatomical resolution, what is especially important in the studies of various GPCRs involved in central neurotransmission.
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Cantini F, Banci L. Structural Knowledge for Molecular Optimization: The Cases of Metal-Mediated Protein-Protein Interactions and Structural Vaccinology. Eur J Inorg Chem 2018. [DOI: 10.1002/ejic.201800699] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Francesca Cantini
- Magnetic Resonance Center (CERM); University of Florence; Via L. Sacconi 6 50019 Sesto Fiorentino Italy
- Department of Chemistry; University of Florence; Via della Lastruccia 3 50019 Sesto Fiorentino Italy
| | - Lucia Banci
- Magnetic Resonance Center (CERM); University of Florence; Via L. Sacconi 6 50019 Sesto Fiorentino Italy
- Department of Chemistry; University of Florence; Via della Lastruccia 3 50019 Sesto Fiorentino Italy
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46
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Lobysheva E, Taylor CM, Marshall GR, Kisselev OG. Tauroursodeoxycholic acid binds to the G-protein site on light activated rhodopsin. Exp Eye Res 2018; 170:51-57. [PMID: 29454859 PMCID: PMC5983371 DOI: 10.1016/j.exer.2018.02.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 02/14/2018] [Accepted: 02/14/2018] [Indexed: 12/18/2022]
Abstract
The heterotrimeric G-protein binding site on G-protein coupled receptors remains relatively unexplored regarding its potential as a new target of therapeutic intervention or as a secondary site of action by the existing drugs. Tauroursodeoxycholic acid bears structural resemblance to several compounds that were previously identified to specifically bind to the light-activated form of the visual receptor rhodopsin and to inhibit its activation of transducin. We show that TUDCA stabilizes the active form of rhodopsin, metarhodopsin II, and does not display the detergent-like effects of common amphiphilic compounds that share the cholesterol scaffold structure, such as deoxycholic acid. Computer docking of TUDCA to the model of light-activated rhodopsin revealed that it interacts using similar mode of binding to the C-terminal domain of transducin alpha subunit. The ring regions of TUDCA made hydrophobic contacts with loop 3 region of rhodopsin, while the tail of TUDCA is exposed to solvent. The results show that TUDCA interacts specifically with rhodopsin, which may contribute to its wide-ranging effects on retina physiology and as a potential therapeutic compound for retina degenerative diseases.
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Affiliation(s)
- E Lobysheva
- Department of Ophthalmology, Saint Louis University School of Medicine, Saint Louis, MO 63104, USA
| | - C M Taylor
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - G R Marshall
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - O G Kisselev
- Department of Ophthalmology, Saint Louis University School of Medicine, Saint Louis, MO 63104, USA.
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Mani T, Bourguinat C, Prichard RK. G-protein-coupled receptor genes of Dirofilaria immitis. Mol Biochem Parasitol 2018; 222:6-13. [PMID: 29625152 DOI: 10.1016/j.molbiopara.2018.04.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 02/28/2018] [Accepted: 04/02/2018] [Indexed: 12/27/2022]
Abstract
The diversity and uniqueness of nematode heterotrimeric G-protein-coupled receptors (GPCRs) provides impetus for identifying ligands that can be used as therapeutics for treating diseases caused by parasitic nematode infections. In human medicine, GPCRs have represented the largest group of 'drugable' targets exploited in the market today. In the filarial nematode Dirofilaria immitis, which causes heartworm disease, the macrocyclic lactones (ML) have been used as the sole preventatives for more than 25 years and now there is confirmed ML resistance in this parasite. A novel anthelmintic emodepside, with antifilarial activity, can act on a GPCR. In view of the ML resistance, there is an urgent need to identify new drug targets and GPCRs of D. immitis may be promising receptors. Knowledge of polymorphism within the GPCR superfamily is of interest. A total of 127 GPCR genes have been identified, so far, in the genome of D. immitis. Whole genome sequencing data from four ML susceptible and four ML loss of efficacy populations was used to identify 393 polymorphic loci in 35 D. immitis GPCR genes. Out of 57 SNPs in exonic regions, 36 of them caused a change in an amino acid, out of which 2 changed the predicted secondary structure of the protein. Knowledge about GPCR genes and their polymorphism is valuable information for drug design processes. Further studies need to be carried out to more fully understand the implications of each of the SNPs identified by this study.
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Affiliation(s)
- Thangadurai Mani
- Institute of Parasitology, McGill University, 21111 Lakeshore Road, Sainte-Anne-de-Bellevue, QC H9X 3V9, Canada
| | - Catherine Bourguinat
- Institute of Parasitology, McGill University, 21111 Lakeshore Road, Sainte-Anne-de-Bellevue, QC H9X 3V9, Canada
| | - Roger K Prichard
- Institute of Parasitology, McGill University, 21111 Lakeshore Road, Sainte-Anne-de-Bellevue, QC H9X 3V9, Canada.
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Trivellin G, Hernández-Ramírez LC, Swan J, Stratakis CA. An orphan G-protein-coupled receptor causes human gigantism and/or acromegaly: Molecular biology and clinical correlations. Best Pract Res Clin Endocrinol Metab 2018; 32:125-140. [PMID: 29678281 DOI: 10.1016/j.beem.2018.02.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
X-linked acrogigantism (X-LAG) is a recently described form of familial or sporadic pituitary gigantism characterized by very early onset GH and IGF-1 excess, accelerated growth velocity, gigantism and/or acromegaloid features. Germline or somatic microduplications of the Xq26.3 chromosomal region, invariably involving the GPR101 gene, constitute the genetic defect leading to X-LAG. GPR101 encodes a class A G protein-coupled receptor that activates the 3',5'-cyclic adenosine monophosphate signaling pathway. Highly expressed in the central nervous system, the main physiological function and ligand of GPR101 remain unknown, but it seems to play a role in the normal development of the GHRH-GH axis. Early recognition of X-LAG cases is imperative because these patients require clinical management that differs from that of other patients with acromegaly or gigantism. Medical treatment with pegvisomant seems to be the best approach, since X-LAG tumors are resistant to the treatment with somatostatin analogues and dopamine agonists; surgical cure requires near-total hypophysectomy. Currently, the efforts of our research focus on the identification of GPR101 ligands; in addition, the long-term follow-up of X-LAG patients is of extreme interest as this is expected to lead to better understanding of GPR101 effects on human pathophysiology.
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Affiliation(s)
- Giampaolo Trivellin
- Section on Endocrinology and Genetics (SEGEN), Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, 20892-1862, USA
| | - Laura C Hernández-Ramírez
- Section on Endocrinology and Genetics (SEGEN), Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, 20892-1862, USA
| | - Jeremy Swan
- Computer Support Services Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, 20892-1862, USA
| | - Constantine A Stratakis
- Section on Endocrinology and Genetics (SEGEN), Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, 20892-1862, USA.
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Le Ferrec E, Øvrevik J. G-protein coupled receptors (GPCR) and environmental exposure. Consequences for cell metabolism using the β-adrenoceptors as example. CURRENT OPINION IN TOXICOLOGY 2018. [DOI: 10.1016/j.cotox.2017.11.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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