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Slane EG, Tambrini SJ, Cummings BS. Therapeutic potential of lipin inhibitors for the treatment of cancer. Biochem Pharmacol 2024; 222:116106. [PMID: 38442792 DOI: 10.1016/j.bcp.2024.116106] [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: 12/18/2023] [Revised: 01/28/2024] [Accepted: 03/01/2024] [Indexed: 03/07/2024]
Abstract
Lipins are phosphatidic acid phosphatases (PAP) that catalyze the conversion of phosphatidic acid (PA) to diacylglycerol (DAG). Three lipin isoforms have been identified: lipin-1, -2 and -3. In addition to their PAP activity, lipin-1 and -2 act as transcriptional coactivators and corepressors. Lipins have been intensely studied for their role in regulation of lipid metabolism and adipogenesis; however, lipins are hypothesized to mediate several pathologies, such as those involving metabolic diseases, neuropathy and even cognitive impairment. Recently, an emerging role for lipins have been proposed in cancer. The study of lipins in cancer has been hampered by lack of inhibitors that have selectivity for lipins, that differentiate between lipin family members, or that are suitable for in vivo studies. Such inhibitors have the potential to be extremely useful as both molecular tools and therapeutics. This review describes the expression and function of lipins in various tissues and their roles in several diseases, but with an emphasis on their possible role in cancer. The mechanisms by which lipins mediate cancer cell growth are discussed and the potential usefulness of selective lipin inhibitors is hypothesized. Finally, recent studies reporting the crystallization of lipin-1 are discussed to facilitate rational design of novel lipin inhibitors.
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Affiliation(s)
- Elizabeth G Slane
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI 48201, USA
| | - Samantha J Tambrini
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI 48201, USA
| | - Brian S Cummings
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI 48201, USA.
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2
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Nakhjavani M, Smith E, Yeo K, Tomita Y, Price TJ, Yool A, Townsend AR, Hardingham JE. Differential antiangiogenic and anticancer activities of the active metabolites of ginsenoside Rg3. J Ginseng Res 2024; 48:171-180. [PMID: 38465222 PMCID: PMC10920002 DOI: 10.1016/j.jgr.2021.05.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 05/18/2021] [Accepted: 05/24/2021] [Indexed: 01/09/2023] Open
Abstract
Background Epimers of ginsenoside Rg3 (Rg3) have a low bioavailability and are prone to deglycosylation, which produces epimers of ginsenoside Rh2 (S-Rh2 and R-Rh2) and protopanaxadiol (S-PPD and R-PPD). The aim of this study was to compare the efficacy and potency of these molecules as anti-cancer agents. Methods Crystal violet staining was used to study the anti-proliferatory action of the molecules on a human epithelial breast cancer cell line, MDA-MB-231, and human umbilical vein endothelial cells (HUVEC) and compare their potency. Cell death and cell cycle were studied using flow cytometry and mode of cell death was studied using live cell imaging. Anti-angiogenic effects of the drug were studied using loop formation assay. Molecular docking showed the interaction of these molecules with vascular endothelial growth factor receptor-2 (VEGFR2) and aquaporin (AQP) water channels. VEGF bioassay was used to study the interaction of Rh2 with VEGFR2, in vitro. Results HUVEC was the more sensitive cell line to the anti-proliferative effects of S-Rh2, S-PPD and R-PPD. The molecules induced necroptosis/necrosis in MDA-MB-231 and apoptosis in HUVEC. S-Rh2 was the most potent inhibitor of loop formation. In silico molecular docking predicted a good binding score between Rh2 or PPD and the ATP-binding pocket of VEGFR2. VEGF bioassay showed that Rh2 was an allosteric modulator of VEGFR2. In addition, SRh2 and PPD had good binding scores with AQP1 and AQP5, both of which play roles in cell migration and proliferation. Conclusion The combination of these molecules might be responsible for the anti-cancer effects observed by Rg3.
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Affiliation(s)
- Maryam Nakhjavani
- Molecular Oncology, Basil Hetzel Institute for Translational Health Research, The Queen Elizabeth Hospital, Woodville South, SA, Australia
| | - Eric Smith
- Molecular Oncology, Basil Hetzel Institute for Translational Health Research, The Queen Elizabeth Hospital, Woodville South, SA, Australia
- Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
| | - Kenny Yeo
- Molecular Oncology, Basil Hetzel Institute for Translational Health Research, The Queen Elizabeth Hospital, Woodville South, SA, Australia
- Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
| | - Yoko Tomita
- Molecular Oncology, Basil Hetzel Institute for Translational Health Research, The Queen Elizabeth Hospital, Woodville South, SA, Australia
- Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
- Medical Oncology Unit, The Queen Elizabeth Hospital, Woodville South, SA, Australia
| | - Timothy J. Price
- Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
- Medical Oncology Unit, The Queen Elizabeth Hospital, Woodville South, SA, Australia
| | - Andrea Yool
- Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
| | - Amanda R. Townsend
- Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
- Medical Oncology Unit, The Queen Elizabeth Hospital, Woodville South, SA, Australia
| | - Jennifer E. Hardingham
- Molecular Oncology, Basil Hetzel Institute for Translational Health Research, The Queen Elizabeth Hospital, Woodville South, SA, Australia
- Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
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3
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Zerihun M, Rubin SJS, Silnitsky S, Qvit N. An Update on Protein Kinases as Therapeutic Targets-Part II: Peptides as Allosteric Protein Kinase C Modulators Targeting Protein-Protein Interactions. Int J Mol Sci 2023; 24:17504. [PMID: 38139336 PMCID: PMC10743673 DOI: 10.3390/ijms242417504] [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: 11/01/2023] [Revised: 12/11/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
Human protein kinases are highly-sought-after drug targets, historically harnessed for treating cancer, cardiovascular disease, and an increasing number of autoimmune and inflammatory conditions. Most current treatments involve small molecule protein kinase inhibitors that interact orthosterically with the protein kinase ATP-binding pocket. As a result, these compounds are often poorly selective and highly toxic. Part I of this series reviews the role of PKC isoforms in various human diseases, featuring cancer and cardiovascular disease, as well as translational examples of PKC modulation applied to human health and disease. In the present Part II, we discuss alternative allosteric binding mechanisms for targeting PKC, as well as novel drug platforms, such as modified peptides. A major goal is to design protein kinase modulators with enhanced selectivity and improved pharmacological properties. To this end, we use molecular docking analysis to predict the mechanisms of action for inhibitor-kinase interactions that can facilitate the development of next-generation PKC modulators.
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Affiliation(s)
- Mulate Zerihun
- The Azrieli Faculty of Medicine in the Galilee, Bar-Ilan University, Henrietta Szold St. 8, P.O. Box 1589, Safed 1311502, Israel; (M.Z.); (S.S.)
| | - Samuel J. S. Rubin
- Department of Medicine, School of Medicine, Stanford University, 300 Pasteur Drive, Stanford, CA 94305, USA;
| | - Shmuel Silnitsky
- The Azrieli Faculty of Medicine in the Galilee, Bar-Ilan University, Henrietta Szold St. 8, P.O. Box 1589, Safed 1311502, Israel; (M.Z.); (S.S.)
| | - Nir Qvit
- The Azrieli Faculty of Medicine in the Galilee, Bar-Ilan University, Henrietta Szold St. 8, P.O. Box 1589, Safed 1311502, Israel; (M.Z.); (S.S.)
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4
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Tian H, Xiao S, Jiang X, Tao P. PASSerRank: Prediction of allosteric sites with learning to rank. J Comput Chem 2023; 44:2223-2229. [PMID: 37561047 PMCID: PMC11127606 DOI: 10.1002/jcc.27193] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 06/19/2023] [Accepted: 07/10/2023] [Indexed: 08/11/2023]
Abstract
Allostery plays a crucial role in regulating protein activity, making it a highly sought-after target in drug development. One of the major challenges in allosteric drug research is the identification of allosteric sites. In recent years, many computational models have been developed for accurate allosteric site prediction. Most of these models focus on designing a general rule that can be applied to pockets of proteins from various families. In this study, we present a new approach using the concept of Learning to Rank (LTR). The LTR model ranks pockets based on their relevance to allosteric sites, that is, how well a pocket meets the characteristics of known allosteric sites. After the training and validation on two datasets, the Allosteric Database (ASD) and CASBench, the LTR model was able to rank an allosteric pocket in the top three positions for 83.6% and 80.5% of test proteins, respectively. The model outperforms other common machine learning models with higher F1 scores (0.662 in ASD and 0.608 in CASBench) and Matthews correlation coefficients (0.645 in ASD and 0.589 in CASBench). The trained model is available on the PASSer platform (https://passer.smu.edu) to aid in drug discovery research.
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Affiliation(s)
- Hao Tian
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas, USA
| | - Sian Xiao
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas, USA
| | - Xi Jiang
- Department of Statistics, Southern Methodist University, Dallas, Texas, USA
| | - Peng Tao
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas, USA
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5
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Abdel Rahman DE, Fouad MA, Mohammed ER, El-Zoheiry HH, Abdelrasheed Allam H. Novel VEGFR-2 inhibitors as antiangiogenic and apoptotic agents via paracrine and autocrine cascades: Design, synthesis, and biological evaluation. Bioorg Chem 2023; 139:106678. [PMID: 37354661 DOI: 10.1016/j.bioorg.2023.106678] [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: 04/18/2023] [Revised: 05/31/2023] [Accepted: 06/12/2023] [Indexed: 06/26/2023]
Abstract
Appertaining to its paracrine and autocrine signaling loops, VEGFR-2 succeeded in grabbing attention as one of the leading targets in cancer treatment. Based on the foregoing and our comprehensive studies regarding pharmacophoric features and activity of sorafenib, novel phenylpyridazinone based VEGFR-2 inhibitors 4, 6a-e, 7a,b, 9a,b, 12a-c, 13a,b, 14a,b, 15a,b, and 17a-d were optimized. An assortment of biological assays was conducted to assess the antiangiogenic and apoptotic activities of the synthesized derivatives. In vitro VEGFR-2 kinase assay verified the inhibitory activity of the synthesized derivatives with IC50 values from 49.1 to 418.0 nM relative to the reference drug sorafenib (IC50 = 81.8 nM). Antiproliferative activity against HUVECs revealed that compounds 2-{2-[2-(6-oxo-3-phenylpyridazin-1(6H)-yl)acetyl]hydrazineyl}-N-(p-tolyl)acetamide (12c) and 2-[(5-mercapto-4-methyl-4H-1,2,4-triazol-3-yl)methyl]-6-phenylpyridazin-3(2H)-one (13a) possessed superior activity (IC50 values = 11.5 and 12.3 nM, respectively) in comparison to sorafenib (IC50 = 23.2 nM). For the purpose of appraising their antiproliferative effect, derivatives 12c and 13a were exposed to cell cycle analysis, apoptotic, cell invasion and migration assays in addition to determination of VEGFR-2 in protein level. Moreover, cytotoxicity as well as selectivity index against WI-38 cell line was measured to examine safety of derivatives 12c and 13a. After that, molecular docking study was executed on the top five compounds in the in vitro VEGFR-2 kinase assay 6d, 12c, 13a, 14a and 17c to get a deep perception on binding mode of the synthesized compounds and correlate the design strategy with biological results. Finally, physicochemical, pharmacokinetic properties, and drug-likeness studies were performed on the top five derivative in in vitro VEGFR-2 kinase assay.
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Affiliation(s)
- Doaa E Abdel Rahman
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Cairo University, Kasr El-Aini St., Cairo 11562, Egypt
| | - Marwa A Fouad
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Cairo University, Kasr El-Aini St., Cairo 11562, Egypt; Pharmaceutical Chemistry Department, School of Pharmacy, New Giza University, Newgiza, km 22 Cairo-Alexandria Desert Road, Cairo, Egypt
| | - Eman R Mohammed
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Cairo University, Kasr El-Aini St., Cairo 11562, Egypt
| | - Haidy H El-Zoheiry
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Cairo University, Kasr El-Aini St., Cairo 11562, Egypt.
| | - Heba Abdelrasheed Allam
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Cairo University, Kasr El-Aini St., Cairo 11562, Egypt
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6
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Allosteric Antagonism of the Pregnane X Receptor (PXR): Current-State-of-the-Art and Prediction of Novel Allosteric Sites. Cells 2022; 11:cells11192974. [PMID: 36230936 PMCID: PMC9563780 DOI: 10.3390/cells11192974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/20/2022] [Accepted: 09/20/2022] [Indexed: 11/26/2022] Open
Abstract
The pregnane X receptor (PXR, NR1I2) is a xenobiotic-activated transcription factor with high levels of expression in the liver. It not only plays a key role in drug metabolism and elimination, but also promotes tumor growth, drug resistance, and metabolic diseases. It has been proposed as a therapeutic target for type II diabetes, metabolic syndrome, and inflammatory bowel disease, and PXR antagonists have recently been considered as a therapy for colon cancer. There are currently no PXR antagonists that can be used in a clinical setting. Nevertheless, due to the large and complex ligand-binding pocket (LBP) of the PXR, it is challenging to discover PXR antagonists at the orthosteric site. Alternative ligand binding sites of the PXR have also been proposed and are currently being studied. Recently, the AF-2 allosteric binding site of the PXR has been identified, with several compounds modulating the site discovered. Herein, we aimed to summarize our current knowledge of allosteric modulation of the PXR as well as our attempt to unlock novel allosteric sites. We describe the novel binding function 3 (BF-3) site of PXR, which is also common for other nuclear receptors. In addition, we also mention a novel allosteric site III based on in silico prediction. The identified allosteric sites of the PXR provide new insights into the development of safe and efficient allosteric modulators of the PXR receptor. We therefore propose that novel PXR allosteric sites might be promising targets for treating chronic metabolic diseases and some cancers.
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7
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Potential and Therapeutic Roles of Diosmin in Human Diseases. Biomedicines 2022; 10:biomedicines10051076. [PMID: 35625813 PMCID: PMC9138579 DOI: 10.3390/biomedicines10051076] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 04/26/2022] [Accepted: 04/27/2022] [Indexed: 12/21/2022] Open
Abstract
Because of their medicinal characteristics, effectiveness, and importance, plant-derived flavonoids have been a possible subject of research for many years, particularly in the last decade. Plants contain a huge number of flavonoids, and Diosmin, a flavone glycoside, is one of them. Numerous in-vitro and in-vivo studies have validated Diosmin’s extensive range of biological capabilities which present antioxidative, antihyperglycemic, anti-inflammatory, antimutagenic, and antiulcer properties. We have presented this review work because of the greater biological properties and influences of Diosmin. We have provided a brief overview of Diosmin, its pharmacology, major biological properties, such as anti-cancer, anti-diabetic, antibacterial, anticardiovascular, liver protection, and neuroprotection, therapeutic approach, potential Diosmin targets, and pathways that are known to be associated with it.
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8
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Combarnous Y, Nguyen TMD. Membrane Hormone Receptors and Their Signaling Pathways as Targets for Endocrine Disruptors. J Xenobiot 2022; 12:64-73. [PMID: 35466213 PMCID: PMC9036253 DOI: 10.3390/jox12020007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 03/14/2022] [Accepted: 03/21/2022] [Indexed: 12/19/2022] Open
Abstract
The endocrine disruptors are mostly small organic molecules developed for numerous and very diverse industrial applications. They essentially act through nuclear receptors with small and hydrophobic endogenous ligands. Nevertheless, potential adverse effects through membrane hormone receptors cannot be ruled out, and have indeed been observed. The present paper reviews how orthosteric and allosteric binding sites of the different families of membrane receptors can be targets for man-made hydrophobic molecules (components of plastics, paints, flame retardants, herbicides, pesticides, etc.). We also review potential target proteins for such small hydrophobic molecules downstream of membrane receptors at the level of their intracellular signaling pathways. From the currently available information, although endocrine disruptors primarily affect nuclear receptors’ signaling, membrane receptors for hormones, cytokines, neuro-mediators, and growth factors can be affected as well and deserve attention.
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Affiliation(s)
- Yves Combarnous
- INRAe, CNRS, Tours University Joint Unit, Physiologie de la Reproduction et des Comportements, 37380 Nouzilly, France;
- Correspondence: ; Tel.: +33-(0)24-7427-650
| | - Thi Mong Diep Nguyen
- INRAe, CNRS, Tours University Joint Unit, Physiologie de la Reproduction et des Comportements, 37380 Nouzilly, France;
- Faculty of Natural Sciences, Quy Nhon University, Quy Nhon 820000, Vietnam
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9
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Pei H, Guo W, Peng Y, Xiong H, Chen Y. Targeting key proteins involved in transcriptional regulation for cancer therapy: Current strategies and future prospective. Med Res Rev 2022; 42:1607-1660. [PMID: 35312190 DOI: 10.1002/med.21886] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/10/2022] [Accepted: 02/22/2022] [Indexed: 12/14/2022]
Abstract
The key proteins involved in transcriptional regulation play convergent roles in cellular homeostasis, and their dysfunction mediates aberrant gene expressions that underline the hallmarks of tumorigenesis. As tumor progression is dependent on such abnormal regulation of transcription, it is important to discover novel chemical entities as antitumor drugs that target key tumor-associated proteins involved in transcriptional regulation. Despite most key proteins (especially transcription factors) involved in transcriptional regulation are historically recognized as undruggable targets, multiple targeting approaches at diverse levels of transcriptional regulation, such as epigenetic intervention, inhibition of DNA-binding of transcriptional factors, and inhibition of the protein-protein interactions (PPIs), have been established in preclinically or clinically studies. In addition, several new approaches have recently been described, such as targeting proteasomal degradation and eliciting synthetic lethality. This review will emphasize on accentuating these developing therapeutic approaches and provide a thorough conspectus of the drug development to target key proteins involved in transcriptional regulation and their impact on future oncotherapy.
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Affiliation(s)
- Haixiang Pei
- Institute for Advanced Study, Shenzhen University and Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Shenzhen University Health Science Center, Shenzhen, China.,Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
| | - Weikai Guo
- Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China.,Joint National Laboratory for Antibody Drug Engineering, School of Basic Medical Science, Henan University, Kaifeng, China
| | - Yangrui Peng
- Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
| | - Hai Xiong
- Institute for Advanced Study, Shenzhen University and Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Shenzhen University Health Science Center, Shenzhen, China
| | - Yihua Chen
- Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
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10
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Hany R, Leyris JP, Bret G, Mallié S, Sar C, Thouaye M, Hamze A, Provot O, Sokoloff P, Valmier J, Villa P, Rognan D. High-Throughput Screening for Extracellular Inhibitors of the FLT3 Receptor Tyrosine Kinase Reveals Chemically Diverse and Druggable Negative Allosteric Modulators. ACS Chem Biol 2022; 17:709-722. [PMID: 35227060 DOI: 10.1021/acschembio.2c00048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Inhibiting receptor tyrosine kinases is commonly achieved by two main strategies targeting either the intracellular kinase domain by low molecular weight compounds or the extracellular ligand-binding domain by monoclonal antibodies. Identifying small molecules able to inhibit RTKs at the extracellular level would be highly desirable to gain exquisite selectivity but is believed to be challenging owing to the size of RTK endogenous ligands (cytokines, growth factors) and the topology of RTK extracellular domains. We here report the high-throughput screening of the French Chemical Library (48K compounds) for extracellular inhibitors of the Fms-like tyrosine kinase 3 (FLT3) receptor tyrosine kinase, by a homogeneous time-resolved fluorescence competition assay. A total of 679 small molecular weight ligands (1.4%) were confirmed to strongly inhibit (>75%) the binding of the fluorescent labeled FLT3 ligand (FL cytokine) to FLT3 overexpressed in HEK-293 cells, at two different concentrations (5 and 20 μM). Concentration-response curves, obtained for 111 lead-like molecules, confirmed the unexpected tolerance of the FLT3 extracellular domain for low molecular weight druggable inhibitors exhibiting submicromolar potencies, chemical diversity, and promising pharmacokinetic properties. Further investigation of one hit confirmed inhibitory properties in dorsal root ganglia neurons and in a mouse model of neuropathic pain.
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Affiliation(s)
- Romain Hany
- Plate-forme de Chimie Biologique Intégrative de Strasbourg (PCBIS), UAR3286 CNRS-Université de Strasbourg, Institut du Médicament de Strasbourg, ESBS Pôle API, Bld Sébastien Brant, 67412 Illkirch Cedex, France
| | - Jean-Philippe Leyris
- Institut des Neurosciences de Montpellier (INM), INSERM, Institut National de la Santé et de la Recherche Médicale, UMR1051, Hôpital Saint-Eloi, 34000 Montpellier, France
- Université de Montpellier, 34000 Montpellier, France
- BIODOL Therapeutics, CAP Alpha, 34830 Clapiers, France
| | - Guillaume Bret
- Laboratoire d’Innovation Thérapeutique (LIT), UMR7200 CNRS-Université de Strasbourg, 67400 Illkirch, France
| | - Sylvie Mallié
- Institut des Neurosciences de Montpellier (INM), INSERM, Institut National de la Santé et de la Recherche Médicale, UMR1051, Hôpital Saint-Eloi, 34000 Montpellier, France
- Université de Montpellier, 34000 Montpellier, France
| | - Chamroeun Sar
- Institut des Neurosciences de Montpellier (INM), INSERM, Institut National de la Santé et de la Recherche Médicale, UMR1051, Hôpital Saint-Eloi, 34000 Montpellier, France
- Université de Montpellier, 34000 Montpellier, France
| | - Maxime Thouaye
- Institut des Neurosciences de Montpellier (INM), INSERM, Institut National de la Santé et de la Recherche Médicale, UMR1051, Hôpital Saint-Eloi, 34000 Montpellier, France
- Université de Montpellier, 34000 Montpellier, France
| | - Abdallah Hamze
- Université Paris-Saclay, CNRS, BioCIS, 92290, Châtenay-Malabry, France
| | - Olivier Provot
- Université Paris-Saclay, CNRS, BioCIS, 92290, Châtenay-Malabry, France
| | | | - Jean Valmier
- Institut des Neurosciences de Montpellier (INM), INSERM, Institut National de la Santé et de la Recherche Médicale, UMR1051, Hôpital Saint-Eloi, 34000 Montpellier, France
- Université de Montpellier, 34000 Montpellier, France
| | - Pascal Villa
- Plate-forme de Chimie Biologique Intégrative de Strasbourg (PCBIS), UAR3286 CNRS-Université de Strasbourg, Institut du Médicament de Strasbourg, ESBS Pôle API, Bld Sébastien Brant, 67412 Illkirch Cedex, France
| | - Didier Rognan
- Laboratoire d’Innovation Thérapeutique (LIT), UMR7200 CNRS-Université de Strasbourg, 67400 Illkirch, France
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11
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Wu M, Carballo-Jane E, Zhou H, Zafian P, Dai G, Liu M, Lao J, Kelly T, Shao D, Gorski J, Pissarnitski D, Kekec A, Chen Y, Previs SF, Scapin G, Gomez-Llorente Y, Hollingsworth SA, Yan L, Feng D, Huo P, Walford G, Erion MD, Kelley DE, Lin S, Mu J. Functionally selective signaling and broad metabolic benefits by novel insulin receptor partial agonists. Nat Commun 2022; 13:942. [PMID: 35177603 PMCID: PMC8854621 DOI: 10.1038/s41467-022-28561-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 01/17/2022] [Indexed: 01/09/2023] Open
Abstract
Insulin analogs have been developed to treat diabetes with focus primarily on improving the time action profile without affecting ligand-receptor interaction or functional selectivity. As a result, inherent liabilities (e.g. hypoglycemia) of injectable insulin continue to limit the true therapeutic potential of related agents. Insulin dimers were synthesized to investigate whether partial agonism of the insulin receptor (IR) tyrosine kinase is achievable, and to explore the potential for tissue-selective systemic insulin pharmacology. The insulin dimers induced distinct IR conformational changes compared to native monomeric insulin and substrate phosphorylation assays demonstrated partial agonism. Structurally distinct dimers with differences in conjugation sites and linkers were prepared to deliver desirable IR partial agonist (IRPA). Systemic infusions of a B29-B29 dimer in vivo revealed sharp differences compared to native insulin. Suppression of hepatic glucose production and lipolysis were like that attained with regular insulin, albeit with a distinctly shallower dose-response. In contrast, there was highly attenuated stimulation of glucose uptake into muscle. Mechanistic studies indicated that IRPAs exploit tissue differences in receptor density and have additional distinctions pertaining to drug clearance and distribution. The hepato-adipose selective action of IRPAs is a potentially safer approach for treatment of diabetes.
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MESH Headings
- Adipose Tissue/drug effects
- Adipose Tissue/metabolism
- Alloxan/administration & dosage
- Alloxan/toxicity
- Animals
- Blood Glucose/drug effects
- Blood Glucose/metabolism
- CHO Cells
- Cricetulus
- Diabetes Mellitus, Experimental/blood
- Diabetes Mellitus, Experimental/chemically induced
- Diabetes Mellitus, Experimental/drug therapy
- Diabetes Mellitus, Experimental/metabolism
- Diabetes Mellitus, Type 1/blood
- Diabetes Mellitus, Type 1/chemically induced
- Diabetes Mellitus, Type 1/drug therapy
- Diabetes Mellitus, Type 1/metabolism
- HEK293 Cells
- Humans
- Hypoglycemic Agents/pharmacology
- Hypoglycemic Agents/therapeutic use
- Insulin/pharmacology
- Insulin/therapeutic use
- Lipolysis/drug effects
- Liver/drug effects
- Liver/metabolism
- Male
- Mice
- Rats
- Receptor, Insulin/agonists
- Recombinant Proteins/pharmacology
- Recombinant Proteins/therapeutic use
- Signal Transduction/drug effects
- Swine
- Swine, Miniature
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Affiliation(s)
- Margaret Wu
- Merck & Co., Inc., Kenilworth, NJ, 07033, USA
| | | | | | | | - Ge Dai
- Merck & Co., Inc., Kenilworth, NJ, 07033, USA
| | - Mindy Liu
- Merck & Co., Inc., South San Francisco, CA, 94080, USA
| | - Julie Lao
- Merck & Co., Inc., South San Francisco, CA, 94080, USA
| | - Terri Kelly
- Merck & Co., Inc., Kenilworth, NJ, 07033, USA
| | - Dan Shao
- Merck & Co., Inc., South San Francisco, CA, 94080, USA
| | | | | | - Ahmet Kekec
- Merck & Co., Inc., Kenilworth, NJ, 07033, USA
| | - Ying Chen
- Merck & Co., Inc., Kenilworth, NJ, 07033, USA
| | | | | | | | | | - Lin Yan
- Merck & Co., Inc., Kenilworth, NJ, 07033, USA
| | | | - Pei Huo
- Merck & Co., Inc., Kenilworth, NJ, 07033, USA
| | | | | | | | | | - James Mu
- Merck & Co., Inc., South San Francisco, CA, 94080, USA.
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12
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Korkutata M, Agrawal L, Lazarus M. Allosteric Modulation of Adenosine A 2A Receptors as a New Therapeutic Avenue. Int J Mol Sci 2022; 23:ijms23042101. [PMID: 35216213 PMCID: PMC8880556 DOI: 10.3390/ijms23042101] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/11/2022] [Accepted: 02/11/2022] [Indexed: 12/26/2022] Open
Abstract
The therapeutic potential of targeting adenosine A2A receptors (A2ARs) is immense due to their broad expression in the body and central nervous system. The role of A2ARs in cardiovascular function, inflammation, sleep/wake behaviors, cognition, and other primary nervous system functions has been extensively studied. Numerous A2AR agonist and antagonist molecules are reported, many of which are currently in clinical trials or have already been approved for treatment. Allosteric modulators can selectively elicit a physiologic response only where and when the orthosteric ligand is released, which reduces the risk of an adverse effect resulting from A2AR activation. Thus, these allosteric modulators have a potential therapeutic advantage over classical agonist and antagonist molecules. This review focuses on the recent developments regarding allosteric A2AR modulation, which is a promising area for future pharmaceutical research because the list of existing allosteric A2AR modulators and their physiologic effects is still short.
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Affiliation(s)
- Mustafa Korkutata
- Department of Neurology, Division of Sleep Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA;
| | - Lokesh Agrawal
- Molecular Neuroscience Unit, Okinawa Institute of Science and Technology Graduate University, Kunigami-gun, Onna 904-0412, Japan;
| | - Michael Lazarus
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba 305-8575, Japan
- Correspondence: ; Tel.: +81-29-853-3681
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13
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Zhang C, Ma X, Zheng X, Ke Y, Chen K, Liu D, Lu Z, Yang J, Yan H. Programmable allosteric DNA regulations for molecular networks and nanomachines. SCIENCE ADVANCES 2022; 8:eabl4589. [PMID: 35108052 PMCID: PMC8809682 DOI: 10.1126/sciadv.abl4589] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Structure-based molecular regulations have been widely adopted to modulate protein networks in cells and recently developed to control allosteric DNA operations in vitro. However, current examples of programmable allosteric signal transmission through integrated DNA networks are stringently constrained by specific design requirements. Developing a new, more general, and programmable scheme for establishing allosteric DNA networks remains challenging. Here, we developed a general strategy for programmable allosteric DNA regulations that can be finely tuned by varying the dimensions, positions, and number of conformational signals. By programming the allosteric signals, we realized fan-out/fan-in DNA gates and multiple-layer DNA cascading networks, as well as expanding the approach to long-range allosteric signal transmission through tunable DNA origami nanomachines ~100 nm in size. This strategy will enable programmable and complex allosteric DNA networks and nanodevices for nanoengineering, chemical, and biomedical applications displaying sense-compute-actuate molecular functionalities.
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Affiliation(s)
- Cheng Zhang
- School of Computer Science, Key Lab of High Confidence Software Technologies, Peking University, Beijing 100871, China
- Corresponding author. (C.Z.); (J.Y.); (H.Y.)
| | - Xueying Ma
- School of Control and Computer Engineering, North China Electric Power University, Beijing 102206, China
- Bio-evidence Sciences Academy, Xi’an Jiaotong University, Xi’an, Shaanxi 710049, China
| | - Xuedong Zheng
- College of Computer Science, Shenyang Aerospace University, Shenyang 110136, China
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Emory University School of Medicine, Atlanta, GA 30322, USA
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
| | - Kuiting Chen
- School of Control and Computer Engineering, North China Electric Power University, Beijing 102206, China
| | - Dongsheng Liu
- Key Laboratory of Organic Optoelectronics and Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Zuhong Lu
- The State Key Laboratory of Bioelectronics, Southeast University, Nanjing 211189, China
| | - Jing Yang
- School of Control and Computer Engineering, North China Electric Power University, Beijing 102206, China
- Corresponding author. (C.Z.); (J.Y.); (H.Y.)
| | - Hao Yan
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
- Corresponding author. (C.Z.); (J.Y.); (H.Y.)
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14
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Wu N, Strömich L, Yaliraki SN. Prediction of allosteric sites and signaling: Insights from benchmarking datasets. PATTERNS (NEW YORK, N.Y.) 2022; 3:100408. [PMID: 35079717 PMCID: PMC8767309 DOI: 10.1016/j.patter.2021.100408] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/06/2021] [Accepted: 11/15/2021] [Indexed: 12/12/2022]
Abstract
Allostery is a pervasive mechanism that regulates protein activity through ligand binding at a site different from the orthosteric site. The universality of allosteric regulation complemented by the benefits of highly specific and potentially non-toxic allosteric drugs makes uncovering allosteric sites invaluable. However, there are few computational methods to effectively predict them. Bond-to-bond propensity analysis has successfully predicted allosteric sites in 19 of 20 cases using an energy-weighted atomistic graph. We here extended the analysis onto 432 structures of 146 proteins from two benchmarking datasets for allosteric proteins: ASBench and CASBench. We further introduced two statistical measures to account for the cumulative effect of high-propensity residues and the crucial residues in a given site. The allosteric site is recovered for 127 of 146 proteins (407 of 432 structures) knowing only the orthosteric sites or ligands. The quantitative analysis using a range of statistical measures enables better characterization of potential allosteric sites and mechanisms involved.
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Affiliation(s)
- Nan Wu
- Department of Chemistry, Imperial College London, London W12 0BZ, UK
| | - Léonie Strömich
- Department of Chemistry, Imperial College London, London W12 0BZ, UK
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15
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Yuan J, Jiang C, Wang J, Chen CJ, Hao Y, Zhao G, Feng Z, Xie XQ. In Silico Prediction and Validation of CB2 Allosteric Binding Sites to Aid the Design of Allosteric Modulators. Molecules 2022; 27:molecules27020453. [PMID: 35056767 PMCID: PMC8781014 DOI: 10.3390/molecules27020453] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/01/2022] [Accepted: 01/03/2022] [Indexed: 11/16/2022] Open
Abstract
Although the 3D structures of active and inactive cannabinoid receptors type 2 (CB2) are available, neither the X-ray crystal nor the cryo-EM structure of CB2-orthosteric ligand-modulator has been resolved, prohibiting the drug discovery and development of CB2 allosteric modulators (AMs). In the present work, we mainly focused on investigating the potential allosteric binding site(s) of CB2. We applied different algorithms or tools to predict the potential allosteric binding sites of CB2 with the existing agonists. Seven potential allosteric sites can be observed for either CB2-CP55940 or CB2-WIN 55,212-2 complex, among which sites B, C, G and K are supported by the reported 3D structures of Class A GPCRs coupled with AMs. Applying our novel algorithm toolset-MCCS, we docked three known AMs of CB2 including Ec2la (C-2), trans-β-caryophyllene (TBC) and cannabidiol (CBD) to each site for further comparisons and quantified the potential binding residues in each allosteric binding site. Sequentially, we selected the most promising binding pose of C-2 in five allosteric sites to conduct the molecular dynamics (MD) simulations. Based on the results of docking studies and MD simulations, we suggest that site H is the most promising allosteric binding site. We plan to conduct bio-assay validations in the future.
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Affiliation(s)
- Jiayi Yuan
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA; (J.Y.); (C.J.); (J.W.); (C.-J.C.); (Y.H.); (G.Z.)
- Department of Pharmaceutical Sciences and National Center of Excellence for Computational Drug Abuse Research, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Chen Jiang
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA; (J.Y.); (C.J.); (J.W.); (C.-J.C.); (Y.H.); (G.Z.)
- Department of Pharmaceutical Sciences and National Center of Excellence for Computational Drug Abuse Research, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Junmei Wang
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA; (J.Y.); (C.J.); (J.W.); (C.-J.C.); (Y.H.); (G.Z.)
- Department of Pharmaceutical Sciences and National Center of Excellence for Computational Drug Abuse Research, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Chih-Jung Chen
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA; (J.Y.); (C.J.); (J.W.); (C.-J.C.); (Y.H.); (G.Z.)
- Department of Pharmaceutical Sciences and National Center of Excellence for Computational Drug Abuse Research, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Yixuan Hao
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA; (J.Y.); (C.J.); (J.W.); (C.-J.C.); (Y.H.); (G.Z.)
- Department of Pharmaceutical Sciences and National Center of Excellence for Computational Drug Abuse Research, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Guangyi Zhao
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA; (J.Y.); (C.J.); (J.W.); (C.-J.C.); (Y.H.); (G.Z.)
- Department of Pharmaceutical Sciences and National Center of Excellence for Computational Drug Abuse Research, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Zhiwei Feng
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA; (J.Y.); (C.J.); (J.W.); (C.-J.C.); (Y.H.); (G.Z.)
- Department of Pharmaceutical Sciences and National Center of Excellence for Computational Drug Abuse Research, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA
- Correspondence: (Z.F.); (X.-Q.X.)
| | - Xiang-Qun Xie
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA; (J.Y.); (C.J.); (J.W.); (C.-J.C.); (Y.H.); (G.Z.)
- Department of Pharmaceutical Sciences and National Center of Excellence for Computational Drug Abuse Research, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA
- Correspondence: (Z.F.); (X.-Q.X.)
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16
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Rehman AU, Lu S, Khan AA, Khurshid B, Rasheed S, Wadood A, Zhang J. Hidden allosteric sites and De-Novo drug design. Expert Opin Drug Discov 2021; 17:283-295. [PMID: 34933653 DOI: 10.1080/17460441.2022.2017876] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
INTRODUCTION Hidden allosteric sites are not visible in apo-crystal structures, but they may be visible in holo-structures when a certain ligand binds and maintains the ligand intended conformation. Several computational and experimental techniques have been used to investigate these hidden sites but identifying them remains a challenge. AREAS COVERED This review provides a summary of the many theoretical approaches for predicting hidden allosteric sites in disease-related proteins. Furthermore, promising cases have been thoroughly examined to reveal the hidden allosteric site and its modulator. EXPERT OPINION In the recent past, with the development in scientific techniques and bioinformatics tools, the number of drug targets for complex human diseases has significantly increased but unfortunately most of these targets are undruggable due to several reasons. Alternative strategies such as finding cryptic (hidden) allosteric sites are an attractive approach for exploitation of the discovery of new targets. These hidden sites are difficult to recognize compared to allosteric sites, mainly due to a lack of visibility in the crystal structure. In our opinion, after many years of development, MD simulations are finally becoming successful for obtaining a detailed molecular description of drug-target interaction.
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Affiliation(s)
- Ashfaq Ur Rehman
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Clinical and Fundamental Research Center, Renji Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, China
| | - Shaoyong Lu
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Clinical and Fundamental Research Center, Renji Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, China
| | - Abdul Aziz Khan
- Bio-X Institutes, Key Laboratory for the Genetics of Development and Neuropsychiatric Disorders (Ministry of Education), Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Institute of Psychology and Behavioral Sciences, Shanghai Jiao Tong University, Shanghai, China
| | - Beenish Khurshid
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Salman Rasheed
- National Center for Bioinformatics, Quaid-e-Azam University, Islamabad, Pakistan
| | - Abdul Wadood
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Jian Zhang
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Clinical and Fundamental Research Center, Renji Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, China.,School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
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17
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Mannes M, Martin C, Menet C, Ballet S. Wandering beyond small molecules: peptides as allosteric protein modulators. Trends Pharmacol Sci 2021; 43:406-423. [PMID: 34857409 DOI: 10.1016/j.tips.2021.10.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/20/2021] [Accepted: 10/26/2021] [Indexed: 12/28/2022]
Abstract
Recent years have seen the rise of allosteric modulation as an innovative approach for drug design and discovery, efforts which culminated in the development of several clinical candidates. Allosteric modulation of many drug targets, including mainly membrane-embedded receptors, have been vastly explored through small molecule screening campaigns, but much less attention has been paid to peptide-based allosteric modulators. However, peptides have a significant impact on the pharmaceutical industry due to the typically higher potency and selectivity for their targets, as compared with small molecule therapeutics. Therefore, peptides represent one of the most promising classes of molecules that can modulate key biological pathways. Here, we report on the allosteric modulation of proteins (ranging from G protein-coupled receptors to specific protein-protein interactions) by peptides for applications in drug discovery.
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Affiliation(s)
- Morgane Mannes
- Research Group of Organic Chemistry, Vrije Universiteit Brussel, Pleinlaan 2, Brussels, Belgium
| | - Charlotte Martin
- Research Group of Organic Chemistry, Vrije Universiteit Brussel, Pleinlaan 2, Brussels, Belgium.
| | - Christel Menet
- Confo Therapeutics N.V., Technologiepark-Zwijnaarde 30, Ghent, Belgium
| | - Steven Ballet
- Research Group of Organic Chemistry, Vrije Universiteit Brussel, Pleinlaan 2, Brussels, Belgium.
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18
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Abstract
Inspired by allosteric regulation of natural molecules, we present a rational design scheme to build synthetic nucleic acid allosteric nanodevices. The clearly specified conformational states of switches obtained from systematic screening and analyses make the ON-OFF transition clear-cut and quantification ready. Under the rational design scheme, we have developed a series of DNA switches with triplex-forming oligos as allosteric modulators and implemented designated allosteric transitions, allosteric coregulation, and reaction pathway control. In conjunction with toehold-mediated strand displacement, our design scheme has also been applied to synthetic nucleic acid computing including a set of logic operations and complex algorithm.
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Affiliation(s)
- Tianqing Zhang
- School of Life Sciences, Tsinghua University-Peking University Center for Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
| | - Bryan Wei
- School of Life Sciences, Tsinghua University-Peking University Center for Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
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19
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Byun JA, VanSchouwen B, Parikh N, Akimoto M, McNicholl ET, Melacini G. State-selective frustration as a key driver of allosteric pluripotency. Chem Sci 2021; 12:11565-11575. [PMID: 34667558 PMCID: PMC8447923 DOI: 10.1039/d1sc01753e] [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] [Received: 03/26/2021] [Accepted: 07/12/2021] [Indexed: 12/13/2022] Open
Abstract
Allosteric pluripotency arises when an allosteric effector switches from agonist to antagonist depending on the experimental conditions. For example, the Rp-cAMPS ligand of Protein Kinase A (PKA) switches from agonist to antagonist as the MgATP concentration increases and/or the kinase substrate affinity or concentration decreases. Understanding allosteric pluripotency is essential to design effective allosteric therapeutics with minimal side effects. Allosteric pluripotency of PKA arises from divergent allosteric responses of two homologous tandem cAMP-binding domains, resulting in a free energy landscape for the Rp-cAMPS-bound PKA regulatory subunit R1a in which the ground state is kinase inhibition-incompetent and the kinase inhibition-competent state is excited. The magnitude of the free energy difference between the ground non-inhibitory and excited inhibitory states (ΔGR,Gap) relative to the effective free energy of R1a binding to the catalytic subunit of PKA (ΔGR:C) dictates whether the antagonism-to-agonism switch occurs. However, the key drivers of ΔGR,Gap are not fully understood. Here, by analyzing an R1a mutant that selectively silences allosteric pluripotency, we show that a major determinant of ΔGR,Gap unexpectedly arises from state-selective frustration in the ground inhibition-incompetent state of Rp-cAMPS-bound R1a. Such frustration is caused by steric clashes between the phosphate-binding cassette and the helices preceding the lid, which interact with the phosphate and base of Rp-cAMPS, respectively. These clashes are absent in the excited inhibitory state, thus reducing the ΔGR,Gap to values comparable to ΔGR:C, as needed for allosteric pluripotency to occur. The resulting model of allosteric pluripotency is anticipated to assist the design of effective allosteric modulators. The Rp-cAMPS ligand of protein kinase A switches from agonist to antagonist depending on metabolite and proteomic contexts. We show that the state-selective frustration is a key driver of this allosteric pluripotency phenomenon.![]()
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Affiliation(s)
- Jung Ah Byun
- Department of Biochemistry and Biomedical Sciences, McMaster University Hamilton ON L8S 4M1 Canada
| | - Bryan VanSchouwen
- Department of Chemistry and Chemical Biology, McMaster University Hamilton ON L8S 4M1 Canada
| | - Nishi Parikh
- Department of Chemistry and Chemical Biology, McMaster University Hamilton ON L8S 4M1 Canada
| | - Madoka Akimoto
- Department of Chemistry and Chemical Biology, McMaster University Hamilton ON L8S 4M1 Canada
| | - Eric Tyler McNicholl
- Department of Chemistry and Chemical Biology, McMaster University Hamilton ON L8S 4M1 Canada
| | - Giuseppe Melacini
- Department of Biochemistry and Biomedical Sciences, McMaster University Hamilton ON L8S 4M1 Canada .,Department of Chemistry and Chemical Biology, McMaster University Hamilton ON L8S 4M1 Canada
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20
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Wei S, Zhao T, Wang J, Zhai X. Approach in Improving Potency and Selectivity of Kinase Inhibitors: Allosteric Kinase Inhibitors. Mini Rev Med Chem 2021; 21:991-1003. [PMID: 33355051 DOI: 10.2174/1389557521666201222144355] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 09/21/2020] [Accepted: 10/16/2020] [Indexed: 11/22/2022]
Abstract
Allostery is an efficient and particular regulatory mechanism to regulate protein functions. Different from conserved orthosteric sites, allosteric sites have a distinctive functional mechanism to form the complex regulatory network. In drug discovery, kinase inhibitors targeting the allosteric pockets have received extensive attention for the advantages of high selectivity and low toxicity. The approval of trametinib as the first allosteric inhibitor validated that allosteric inhibitors could be used as effective therapeutic drugs for the treatment of diseases. To date, a wide range of allosteric inhibitors have been identified. In this perspective, we outline different binding modes and potential advantages of allosteric inhibitors. In the meantime, the research processes of typical and novel allosteric inhibitors are described briefly in terms of structure-activity relationships, ligand-protein interactions, and in vitro and in vivo activity. Additionally, challenges, as well as opportunities, are also presented.
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Affiliation(s)
- Shangfei Wei
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Tianming Zhao
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Jie Wang
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Xin Zhai
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
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21
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Kakarala KK, Jamil K. Identification of novel allosteric binding sites and multi-targeted allosteric inhibitors of receptor and non-receptor tyrosine kinases using a computational approach. J Biomol Struct Dyn 2021; 40:6889-6909. [PMID: 33682622 DOI: 10.1080/07391102.2021.1891140] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
EGFR1, VEGFR2, Bcr-Abl and Src kinases are key drug targets in non-small cell lung cancer (NSCLC), bladder cancer, pancreatic cancer, CML, ALL, colorectal cancer, etc. The available drugs targeting these kinases have limited therapeutic efficacy due to novel mutations resulting in drug resistance and toxicity, as they target ATP binding site. Allosteric drugs have shown promising results in overcoming drug resistance, but the discovery of allosteric drugs is challenging. The allosteric binding pockets are difficult to predict, as they are generally associated with high energy conformations and regulate protein function in yet unknown mechanisms. In addition, the discovery of drugs using conventional methods takes long time and goes through several challenges, putting the lives of many cancer patients at risk. Therefore, the aim of the present work was to apply the most successful, drug repurposing approach in combination with computational methods to identify kinase inhibitors targeting novel allosteric sites on protein structure and assess their potential multi-kinase binding affinity. Multiple crystal structures belonging to EGFR1, VEGFR2, Bcr-Abl and Src tyrosine kinases were selected, including mutated, inhibitor bound and allosteric conformations to identify potential leads, close to physiological conditions. Interestingly the potential inhibitors identified were peptides. The drugs identified in this study could be used in therapy as a single multi-kinase inhibitor or in a combination of single kinase inhibitors after experimental validation. In addition, we have also identified new hot spots that are likely to be druggable allosteric sites for drug discovery of kinase-specific drugs in the future.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Kaiser Jamil
- Bhagwan Mahavir Medical Research Center, Hyderabad, Telangana, India
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22
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Yunn NO, Park M, Park S, Lee J, Noh J, Shin E, Ryu SH. A hotspot for enhancing insulin receptor activation revealed by a conformation-specific allosteric aptamer. Nucleic Acids Res 2021; 49:700-712. [PMID: 33410883 PMCID: PMC7826266 DOI: 10.1093/nar/gkaa1247] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 11/23/2020] [Accepted: 12/15/2020] [Indexed: 01/20/2023] Open
Abstract
Aptamers are single-stranded oligonucleotides that bind to a specific target with high affinity, and are widely applied in biomedical diagnostics and drug development. However, the use of aptamers has largely been limited to simple binders or inhibitors that interfere with the function of a target protein. Here, we show that an aptamer can also act as a positive allosteric modulator that enhances the activation of a receptor by stabilizing the binding of a ligand to that receptor. We developed an aptamer, named IR-A43, which binds to the insulin receptor, and confirmed that IR-A43 and insulin bind to the insulin receptor with mutual positive cooperativity. IR-A43 alone is inactive, but, in the presence of insulin, it potentiates autophosphorylation and downstream signaling of the insulin receptor. By using the species-specific activity of IR-A43 at the human insulin receptor, we demonstrate that residue Q272 in the cysteine-rich domain is directly involved in the insulin-enhancing activity of IR-A43. Therefore, we propose that the region containing residue Q272 is a hotspot that can be used to enhance insulin receptor activation. Moreover, our study implies that aptamers are promising reagents for the development of allosteric modulators that discriminate a specific conformation of a target receptor.
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Affiliation(s)
- Na-Oh Yunn
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
| | - Mangeun Park
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
| | - Seongeun Park
- Postech Biotech Center, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
| | - Jimin Lee
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
| | - Jeongeun Noh
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
| | - Euisu Shin
- Aptamer Sciences, Inc., Seongnam 13605, Republic of Korea
| | - Sung Ho Ryu
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea.,School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
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23
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Carli M, Sormani G, Rodriguez A, Laio A. Candidate Binding Sites for Allosteric Inhibition of the SARS-CoV-2 Main Protease from the Analysis of Large-Scale Molecular Dynamics Simulations. J Phys Chem Lett 2021; 12:65-72. [PMID: 33306377 PMCID: PMC7755075 DOI: 10.1021/acs.jpclett.0c03182] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 12/08/2020] [Indexed: 05/20/2023]
Abstract
We analyzed a 100 μs MD trajectory of the SARS-CoV-2 main protease by a non-parametric data analysis approach which allows characterizing a free energy landscape as a simultaneous function of hundreds of variables. We identified several conformations that, when visited by the dynamics, are stable for several hundred nanoseconds. We explicitly characterize and describe these metastable states. In some of these configurations, the catalytic dyad is less accessible. Stabilizing them by a suitable binder could lead to an inhibition of the enzymatic activity. In our analysis we keep track of relevant contacts between residues which are selectively broken or formed in the states. Some of these contacts are formed by residues which are far from the catalytic dyad and are accessible to the solvent. Based on this analysis we propose some relevant contact patterns and three possible binding sites which could be targeted to achieve allosteric inhibition.
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Affiliation(s)
- Matteo Carli
- Scuola
Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 265, 34136 Trieste, Italy
| | - Giulia Sormani
- Scuola
Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 265, 34136 Trieste, Italy
| | - Alex Rodriguez
- The
Abdus Salam International Centre for Theoretical Physics (ICTP), Str. Costiera, 11, 34151 Trieste, Italy
| | - Alessandro Laio
- Scuola
Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 265, 34136 Trieste, Italy
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24
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Wang Y, Yu Z, Xiao W, Lu S, Zhang J. Allosteric binding sites at the receptor-lipid bilayer interface: novel targets for GPCR drug discovery. Drug Discov Today 2020; 26:690-703. [PMID: 33301977 DOI: 10.1016/j.drudis.2020.12.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 10/19/2020] [Accepted: 12/01/2020] [Indexed: 01/01/2023]
Abstract
As a superfamily of membrane receptors, G-protein-coupled receptors (GPCRs) have significant roles in human physiological processes, including cell proliferation, metabolism, and neuromodulation. GPCRs are vital targets of therapeutic drugs, and their allosteric regulation represents a novel direction for drug discovery. Given the numerous breakthroughs in structural biology, diverse allosteric sites on GPCRs have been identified within the extracellular and intracellular loops, and the seven core transmembrane helices. However, a unique type of allosteric site has also been discovered at the interface of the receptor-lipid bilayer, similar to the β2-adrenergic receptor. Here, we review recent identifications of these allosteric sites and the detailed modulator-target interactions within the interface for each modulator to highlight the role of lipids in GPCR allosteric drug discovery.
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Affiliation(s)
- Ying Wang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai, 200025, China
| | - Zhengtian Yu
- Nutshell Biotechnology Co., Ltd., Shanghai, China
| | - Wen Xiao
- Nutshell Biotechnology Co., Ltd., Shanghai, China
| | - Shaoyong Lu
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai, 200025, China; Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China.
| | - Jian Zhang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai, 200025, China; Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China.
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25
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Crudden C, Shibano T, Song D, Dragomir MP, Cismas S, Serly J, Nedelcu D, Fuentes-Mattei E, Tica A, Calin GA, Girnita A, Girnita L. Inhibition of G Protein-Coupled Receptor Kinase 2 Promotes Unbiased Downregulation of IGF1 Receptor and Restrains Malignant Cell Growth. Cancer Res 2020; 81:501-514. [PMID: 33158816 DOI: 10.1158/0008-5472.can-20-1662] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 10/03/2020] [Accepted: 10/30/2020] [Indexed: 11/16/2022]
Abstract
The ability of a receptor to preferentially activate only a subset of available downstream signal cascades is termed biased signaling. Although comprehensively recognized for the G protein-coupled receptors (GPCR), this process is scarcely explored downstream of receptor tyrosine kinases (RTK), including the cancer-relevant insulin-like growth factor-1 receptor (IGF1R). Successful IGF1R targeting requires receptor downregulation, yet therapy-mediated removal from the cell surface activates cancer-protective β-arrestin-biased signaling (β-arr-BS). As these overlapping processes are initiated by the β-arr/IGF1R interaction and controlled by GPCR-kinases (GRK), we explored GRKs as potential anticancer therapeutic targets to disconnect IGF1R downregulation and β-arr-BS. Transgenic modulation demonstrated that GRK2 inhibition or GRK6 overexpression enhanced degradation of IGF1R, but both scenarios sustained IGF1-induced β-arr-BS. Pharmacologic inhibition of GRK2 by the clinically approved antidepressant, serotonin reuptake inhibitor paroxetine (PX), recapitulated the effects of GRK2 silencing with dose- and time-dependent IGF1R downregulation without associated β-arr-BS. In vivo, PX treatment caused substantial downregulation of IGF1R, suppressing the growth of Ewing's sarcoma xenografts. Functional studies reveal that PX exploits the antagonism between β-arrestin isoforms; in low ligand conditions, PX favored β-arrestin1/Mdm2-mediated ubiquitination/degradation of IGF1R, a scenario usually exclusive to ligand abundancy, making PX more effective than antibody-mediated IGF1R downregulation. This study provides the rationale, molecular mechanism, and validation of a clinically feasible concept for "system bias" targeting of the IGF1R to uncouple downregulation from signaling. Demonstrating system bias as an effective anticancer approach, our study reveals a novel strategy for the rational design or repurposing of therapeutics to selectively cross-target the IGF1R or other RTK. SIGNIFICANCE: This work provides insight into the molecular and biological roles of biased signaling downstream RTK and provides a novel "system bias" strategy to increase the efficacy of anti-IGF1R-targeted therapy in cancer.
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Affiliation(s)
- Caitrin Crudden
- Department of Oncology and Pathology, BioClinicum, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden.,Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Takashi Shibano
- Department of Oncology and Pathology, BioClinicum, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Dawei Song
- Department of Oncology and Pathology, BioClinicum, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Mihnea P Dragomir
- Department of Experimental Therapeutics, The University of Texas, MD Anderson Cancer Center, Houston, Texas
| | - Sonia Cismas
- Department of Oncology and Pathology, BioClinicum, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Julianna Serly
- Department of Oncology and Pathology, BioClinicum, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Daniela Nedelcu
- Department of Oncology and Pathology, BioClinicum, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Enrique Fuentes-Mattei
- Department of Experimental Therapeutics, The University of Texas, MD Anderson Cancer Center, Houston, Texas
| | - Andrei Tica
- Department of Pharmacology, University of Medicine and Pharmacy of Craiova, Craiova, Romania
| | - George A Calin
- Department of Experimental Therapeutics, The University of Texas, MD Anderson Cancer Center, Houston, Texas
| | - Ada Girnita
- Department of Oncology and Pathology, BioClinicum, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden.,Dermatology Department, Karolinska University Hospital, Stockholm, Sweden
| | - Leonard Girnita
- Department of Oncology and Pathology, BioClinicum, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden.
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26
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Byun JA, Akimoto M, VanSchouwen B, Lazarou TS, Taylor SS, Melacini G. Allosteric pluripotency as revealed by protein kinase A. SCIENCE ADVANCES 2020; 6:eabb1250. [PMID: 32596469 PMCID: PMC7304965 DOI: 10.1126/sciadv.abb1250] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 05/08/2020] [Indexed: 05/03/2023]
Abstract
The functional response of a signaling system to an allosteric stimulus often depends on subcellular conditions, a phenomenon known as pluripotent allostery. For example, a single allosteric modulator, Rp-cAMPS, of the prototypical protein kinase A (PKA) switches from antagonist to agonist depending on MgATP levels. However, the mechanism underlying such pluripotent allostery has remained elusive for decades. Using nuclear magnetic resonance spectroscopy, ensemble models, kinase assays, and molecular dynamics simulations, we show that allosteric pluripotency arises from surprisingly divergent responses of highly homologous tandem domains. The differential responses perturb domain-domain interactions and remodel the free-energy landscape of inhibitory excited states sampled by the regulatory subunit of PKA. The resulting activation threshold values are comparable to the effective free energy of regulatory and catalytic subunit binding, which depends on metabolites, substrates, and mutations, explaining pluripotent allostery and warranting a general redefinition of allosteric targets to include specific subcellular environments.
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Affiliation(s)
- J. A. Byun
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4M1, Canada
| | - M. Akimoto
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON L8S 4M1, Canada
| | - B. VanSchouwen
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON L8S 4M1, Canada
| | - T. S. Lazarou
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON L8S 4M1, Canada
| | - S. S. Taylor
- Departments of Chemistry and Biochemistry and Pharmacology, University of California San Diego, La Jolla, CA 92093, USA
| | - G. Melacini
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4M1, Canada
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON L8S 4M1, Canada
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27
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Rallabandi HR, Ganesan P, Kim YJ. Targeting the C-Terminal Domain Small Phosphatase 1. Life (Basel) 2020; 10:life10050057. [PMID: 32397221 PMCID: PMC7281111 DOI: 10.3390/life10050057] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 05/05/2020] [Accepted: 05/07/2020] [Indexed: 12/15/2022] Open
Abstract
The human C-terminal domain small phosphatase 1 (CTDSP1/SCP1) is a protein phosphatase with a conserved catalytic site of DXDXT/V. CTDSP1’s major activity has been identified as dephosphorylation of the 5th Ser residue of the tandem heptad repeat of the RNA polymerase II C-terminal domain (RNAP II CTD). It is also implicated in various pivotal biological activities, such as acting as a driving factor in repressor element 1 (RE-1)-silencing transcription factor (REST) complex, which silences the neuronal genes in non-neuronal cells, G1/S phase transition, and osteoblast differentiation. Recent findings have denoted that negative regulation of CTDSP1 results in suppression of cancer invasion in neuroglioma cells. Several researchers have focused on the development of regulating materials of CTDSP1, due to the significant roles it has in various biological activities. In this review, we focused on this emerging target and explored the biological significance, challenges, and opportunities in targeting CTDSP1 from a drug designing perspective.
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28
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Hu S, Ferraro M, Thomas AP, Chung JM, Yoon NG, Seol JH, Kim S, Kim HU, An MY, Ok H, Jung HS, Ryu JH, Colombo G, Kang BH. Dual Binding to Orthosteric and Allosteric Sites Enhances the Anticancer Activity of a TRAP1-Targeting Drug. J Med Chem 2020; 63:2930-2940. [DOI: 10.1021/acs.jmedchem.9b01420] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Sung Hu
- Department of Biological Sciences, Ulsan National Institutes of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Mariarosaria Ferraro
- Istituto di Chimica del Riconoscimento Molecolare (ICRM), Consiglio Nazionale delle Ricerche (CNR), Milan 20131, Italy
| | - Ajesh P. Thomas
- Department of Chemistry, Ulsan National Institutes of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Jeong Min Chung
- Division of Chemistry and Biochemistry, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Nam Gu Yoon
- Department of Biological Sciences, Ulsan National Institutes of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Ji-Hoon Seol
- Department of Chemistry, Ulsan National Institutes of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Sangpil Kim
- Department of Chemistry, Ulsan National Institutes of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Han-ul Kim
- Division of Chemistry and Biochemistry, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Mi Young An
- Division of Chemistry and Biochemistry, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Haewon Ok
- Department of Chemistry, Ulsan National Institutes of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Hyun Suk Jung
- Division of Chemistry and Biochemistry, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Ja-Hyoung Ryu
- Department of Chemistry, Ulsan National Institutes of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Giorgio Colombo
- University of Pavia, Department of Chemistry, Pavia 27100, Italy
| | - Byoung Heon Kang
- Department of Biological Sciences, Ulsan National Institutes of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
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29
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MacKerell AD, Jo S, Lakkaraju SK, Lind C, Yu W. Identification and characterization of fragment binding sites for allosteric ligand design using the site identification by ligand competitive saturation hotspots approach (SILCS-Hotspots). Biochim Biophys Acta Gen Subj 2020; 1864:129519. [PMID: 31911242 DOI: 10.1016/j.bbagen.2020.129519] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 12/21/2019] [Accepted: 12/31/2019] [Indexed: 12/11/2022]
Abstract
BACKGROUND Fragment-based ligand design is used for the development of novel ligands that target macromolecules, most notably proteins. Central to its success is the identification of fragment binding sites that are spatially adjacent such that fragments occupying those sites may be linked to create drug-like ligands. Current experimental and computational approaches that address this problem typically identify only a limited number of sites as well as use a limited number of fragment types. METHODS The site-identification by ligand competitive saturation (SILCS) approach is extended to the identification of fragment bindings sites, with the method termed SILCS-Hotspots. The approach involves precomputation of the SILCS FragMaps following which the identification of Hotspots, performed by identifying of all possible fragment binding sites on the full 3D structure of the protein followed by spatial clustering. RESULTS The SILCS-Hotspots approach identifies a large number of sites on the target protein, including many sites not accessible in experimental structures due to low binding affinities and binding sites on the protein interior. The identified sites are shown to recapitulate the location of known drug-like molecules in both allosteric and orthosteric binding sites on seven proteins including the androgen receptor, the CDK2 and Erk5 kinases, PTP1B phosphatase and three GPCRs; the β2-adrenergic, GPR40 fatty-acid binding and M2-muscarinic receptors. Analysis indicates the importance of considering all possible fragment binding sites, and not just those accessible to experimental methods, when identifying novel binding sites and performing ligand design versus just considering the most favorable sites. The approach is shown to identify a larger number of known binding sites of drug-like molecules versus the commonly used FTMap and Fpocket methods. GENERAL SIGNIFICANCE The present results indicate the potential utility of the SILCS-Hotspots approach for fragment-based rational design of ligands, including allosteric modulators.
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Affiliation(s)
- Alexander D MacKerell
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, MD 21201, United States of America.
| | - Sunhwan Jo
- SilcsBio, LLC, 8 Market Place, Suite 300, Baltimore, MD 21202, United States of America
| | | | - Christoffer Lind
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, MD 21201, United States of America
| | - Wenbo Yu
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, MD 21201, United States of America
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30
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Lu S, He X, Ni D, Zhang J. Allosteric Modulator Discovery: From Serendipity to Structure-Based Design. J Med Chem 2019; 62:6405-6421. [PMID: 30817889 DOI: 10.1021/acs.jmedchem.8b01749] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Shaoyong Lu
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Clinical and Fundamental Research Center, Renji Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai 200025, China
- Medicinal Bioinformatics Center, Shanghai Jiao-Tong University School of Medicine, Shanghai 200025, China
| | - Xinheng He
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Clinical and Fundamental Research Center, Renji Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai 200025, China
| | - Duan Ni
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Clinical and Fundamental Research Center, Renji Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai 200025, China
| | - Jian Zhang
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Clinical and Fundamental Research Center, Renji Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai 200025, China
- Medicinal Bioinformatics Center, Shanghai Jiao-Tong University School of Medicine, Shanghai 200025, China
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31
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Lu S, Shen Q, Zhang J. Allosteric Methods and Their Applications: Facilitating the Discovery of Allosteric Drugs and the Investigation of Allosteric Mechanisms. Acc Chem Res 2019; 52:492-500. [PMID: 30688063 DOI: 10.1021/acs.accounts.8b00570] [Citation(s) in RCA: 112] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Allostery, or allosteric regulation, is the phenomenon in which protein functional activity is altered by the binding of an effector at an allosteric site that is topographically distinct from the orthosteric, active site. As one of the most direct and efficient ways to regulate protein function, allostery has played a fundamental role in innumerable biological processes of all living organisms, including enzyme catalysis, signal transduction, cell metabolism, and gene transcription. It is thus considered as "the second secret of life". The abnormality of allosteric communication networks between allosteric and orthosteric sites is associated with the pathogenesis of human diseases. Allosteric modulators, by attaching to structurally diverse allosteric sites, offer the potential for differential selectivity and improved safety compared with orthosteric drugs that bind to conserved orthosteric sites. Harnessing allostery has thus been regarded as a novel strategy for drug discovery. Despite much progress having been made in the repertoire of allostery since the turn of the millennium, the identification of allosteric drugs for therapeutic targets and the elucidation of allosteric mechanisms still present substantial challenges. These challenges are derived from the difficulties in the identification of allosteric sites and mutations, the assessment of allosteric protein-modulator interactions, the screening of allosteric modulators, and the elucidation of allosteric mechanisms in biological systems. To address these issues, we have developed a panel of allosteric services for specific allosteric applications over the past decade, including (i) the creation of the Allosteric Database, with the aim of providing comprehensive allosteric information such as allosteric proteins, modulators, sites, pathways, etc., (ii) the construction of the ASBench benchmark of high-quality allosteric sites for the development of computational methods for predicting allosteric sites, (iii) the development of Allosite and AllositePro for the prediction of the location of allosteric sites in proteins, (iv) the development of the Alloscore scoring function for the evaluation of allosteric protein-modulator interactions, (v) the development of Allosterome for evolutionary analysis of query allosteric sites/modulators within the human proteome, (vi) the development of AlloDriver for the prediction of allosteric mutagenesis, and (vii) the development of AlloFinder for the virtual screening of allosteric modulators and the investigation of allosteric mechanisms. Importantly, we have validated computationally predicted allosteric sites, mutations, and modulators in the real cases of sirtuin 6, casein kinase 2α, phosphodiesterase 10A, and signal transduction and activation of transcription 3. Furthermore, our developed allosteric methods have been widely exploited by other users around the world for allosteric research. Therefore, these allosteric services are expected to expedite the discovery of allosteric drugs and the investigation of allosteric mechanisms.
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Affiliation(s)
- Shaoyong Lu
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Qiancheng Shen
- Medicinal Bioinformatics Center, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Jian Zhang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
- Medicinal Bioinformatics Center, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
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32
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Payghan PV, Nath Roy S, Bhattacharyya D, Ghoshal N. Cross-talk between allosteric and orthosteric binding sites of γ-amino butyric acid type A receptors (GABAA-Rs): A computational study revealing the structural basis of selectivity. J Biomol Struct Dyn 2019; 37:3065-3080. [DOI: 10.1080/07391102.2018.1508367] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Pavan V. Payghan
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | | | | | - Nanda Ghoshal
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
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33
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Identification of small molecule activators for ErbB 4 receptor to enhance oligodendrocyte regeneration by in silico approach. ACTA ACUST UNITED AC 2018. [DOI: 10.1016/j.comtox.2018.08.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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34
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Kubota R, Nomura W, Iwasaka T, Ojima K, Kiyonaka S, Hamachi I. Chemogenetic Approach Using Ni(II) Complex-Agonist Conjugates Allows Selective Activation of Class A G-Protein-Coupled Receptors. ACS CENTRAL SCIENCE 2018; 4:1211-1221. [PMID: 30276255 PMCID: PMC6161059 DOI: 10.1021/acscentsci.8b00390] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Indexed: 05/04/2023]
Abstract
Investigating individual G-protein-coupled receptors (GPCRs) involved in various signaling cascades can unlock a myriad of invaluable physiological findings. One of the promising strategies for addressing the activity of each subtype of receptor is to design chemical turn-on switches on the target receptors. However, valid methods to selectively control class A GPCRs, the largest receptor family encoded in the human genome, remain limited. Here, we describe a novel approach to chemogenetically manipulate activity of engineered class A GPCRs carrying a His4 tag, using metal complex-agonist conjugates (MACs). This manipulation is termed coordination tethering. With the assistance of coordination bonds, MACs showed 10-100-fold lower EC50 values in the engineered receptors, compared with wild-type receptors. Such coordination tethering enabled selective activation of β2-adrenoceptors and muscarinic acetylcholine receptors, without loss of natural receptor responses, in living mammalian cells, including primary cultured astrocytes. Our generalized, modular chemogenetic approach should facilitate more precise control and deeper understanding of individual GPCR signaling pathways in living systems.
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Affiliation(s)
- Ryou Kubota
- Department
of Synthetic Chemistry and Biological Chemistry, Graduate School of
Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Wataru Nomura
- Department
of Synthetic Chemistry and Biological Chemistry, Graduate School of
Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Takuma Iwasaka
- Department
of Synthetic Chemistry and Biological Chemistry, Graduate School of
Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Kento Ojima
- Department
of Synthetic Chemistry and Biological Chemistry, Graduate School of
Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Shigeki Kiyonaka
- Department
of Synthetic Chemistry and Biological Chemistry, Graduate School of
Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Itaru Hamachi
- Department
of Synthetic Chemistry and Biological Chemistry, Graduate School of
Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
- Core
Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 5 Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
- E-mail:
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35
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Peach CJ, Mignone VW, Arruda MA, Alcobia DC, Hill SJ, Kilpatrick LE, Woolard J. Molecular Pharmacology of VEGF-A Isoforms: Binding and Signalling at VEGFR2. Int J Mol Sci 2018; 19:E1264. [PMID: 29690653 PMCID: PMC5979509 DOI: 10.3390/ijms19041264] [Citation(s) in RCA: 265] [Impact Index Per Article: 44.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 04/14/2018] [Accepted: 04/16/2018] [Indexed: 02/07/2023] Open
Abstract
Vascular endothelial growth factor-A (VEGF-A) is a key mediator of angiogenesis, signalling via the class IV tyrosine kinase receptor family of VEGF Receptors (VEGFRs). Although VEGF-A ligands bind to both VEGFR1 and VEGFR2, they primarily signal via VEGFR2 leading to endothelial cell proliferation, survival, migration and vascular permeability. Distinct VEGF-A isoforms result from alternative splicing of the Vegfa gene at exon 8, resulting in VEGFxxxa or VEGFxxxb isoforms. Alternative splicing events at exons 5⁻7, in addition to recently identified posttranslational read-through events, produce VEGF-A isoforms that differ in their bioavailability and interaction with the co-receptor Neuropilin-1. This review explores the molecular pharmacology of VEGF-A isoforms at VEGFR2 in respect to ligand binding and downstream signalling. To understand how VEGF-A isoforms have distinct signalling despite similar affinities for VEGFR2, this review re-evaluates the typical classification of these isoforms relative to the prototypical, “pro-angiogenic” VEGF165a. We also examine the molecular mechanisms underpinning the regulation of VEGF-A isoform signalling and the importance of interactions with other membrane and extracellular matrix proteins. As approved therapeutics targeting the VEGF-A/VEGFR signalling axis largely lack long-term efficacy, understanding these isoform-specific mechanisms could aid future drug discovery efforts targeting VEGF receptor pharmacology.
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Affiliation(s)
- Chloe J Peach
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK.
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands NG7 2UH, UK.
| | - Viviane W Mignone
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK.
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands NG7 2UH, UK.
- CAPES-University of Nottingham Programme in Drug Discovery, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK.
| | - Maria Augusta Arruda
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK.
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands NG7 2UH, UK.
- CAPES-University of Nottingham Programme in Drug Discovery, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK.
| | - Diana C Alcobia
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK.
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands NG7 2UH, UK.
| | - Stephen J Hill
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK.
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands NG7 2UH, UK.
| | - Laura E Kilpatrick
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK.
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands NG7 2UH, UK.
| | - Jeanette Woolard
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK.
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands NG7 2UH, UK.
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36
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Rivat C, Sar C, Mechaly I, Leyris JP, Diouloufet L, Sonrier C, Philipson Y, Lucas O, Mallié S, Jouvenel A, Tassou A, Haton H, Venteo S, Pin JP, Trinquet E, Charrier-Savournin F, Mezghrani A, Joly W, Mion J, Schmitt M, Pattyn A, Marmigère F, Sokoloff P, Carroll P, Rognan D, Valmier J. Inhibition of neuronal FLT3 receptor tyrosine kinase alleviates peripheral neuropathic pain in mice. Nat Commun 2018. [PMID: 29531216 PMCID: PMC5847526 DOI: 10.1038/s41467-018-03496-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Peripheral neuropathic pain (PNP) is a debilitating and intractable chronic disease, for which sensitization of somatosensory neurons present in dorsal root ganglia that project to the dorsal spinal cord is a key physiopathological process. Here, we show that hematopoietic cells present at the nerve injury site express the cytokine FL, the ligand of fms-like tyrosine kinase 3 receptor (FLT3). FLT3 activation by intra-sciatic nerve injection of FL is sufficient to produce pain hypersensitivity, activate PNP-associated gene expression and generate short-term and long-term sensitization of sensory neurons. Nerve injury-induced PNP symptoms and associated-molecular changes were strongly altered in Flt3-deficient mice or reversed after neuronal FLT3 downregulation in wild-type mice. A first-in-class FLT3 negative allosteric modulator, discovered by structure-based in silico screening, strongly reduced nerve injury-induced sensory hypersensitivity, but had no effect on nociception in non-injured animals. Collectively, our data suggest a new and specific therapeutic approach for PNP. Sensitisation of dorsal root ganglia neurons contributes to neuropathic pain. Here the authors demonstrate the cytokine FL contributes to sensitisation of DRGs via its receptor FLT3 expressed on neurons, and identify a novel FLT3 inhibitor that attenuates neuropathic pain in mice.
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Affiliation(s)
- Cyril Rivat
- Institute for Neurosciences of Montpellier, INSERM, Institut National de la Santé et de la Recherche Médicale, UMR1051, Hôpital Saint-Eloi, Montpellier, 34000, France.,Université de Montpellier, Montpellier, 34000, France
| | - Chamroeun Sar
- Institute for Neurosciences of Montpellier, INSERM, Institut National de la Santé et de la Recherche Médicale, UMR1051, Hôpital Saint-Eloi, Montpellier, 34000, France.,Université de Montpellier, Montpellier, 34000, France
| | - Ilana Mechaly
- Institute for Neurosciences of Montpellier, INSERM, Institut National de la Santé et de la Recherche Médicale, UMR1051, Hôpital Saint-Eloi, Montpellier, 34000, France.,Université de Montpellier, Montpellier, 34000, France
| | - Jean-Philippe Leyris
- Institute for Neurosciences of Montpellier, INSERM, Institut National de la Santé et de la Recherche Médicale, UMR1051, Hôpital Saint-Eloi, Montpellier, 34000, France.,Biodol Therapeutics, Cap Alpha, Clapiers, 34830, France
| | - Lucie Diouloufet
- Institute for Neurosciences of Montpellier, INSERM, Institut National de la Santé et de la Recherche Médicale, UMR1051, Hôpital Saint-Eloi, Montpellier, 34000, France
| | - Corinne Sonrier
- Institute for Neurosciences of Montpellier, INSERM, Institut National de la Santé et de la Recherche Médicale, UMR1051, Hôpital Saint-Eloi, Montpellier, 34000, France.,Biodol Therapeutics, Cap Alpha, Clapiers, 34830, France
| | - Yann Philipson
- Laboratoire d'Innovation Thérapeutique, UMR7200, CNRS-Université de Strasbourg, Illkirch, 67400, France
| | - Olivier Lucas
- Institute for Neurosciences of Montpellier, INSERM, Institut National de la Santé et de la Recherche Médicale, UMR1051, Hôpital Saint-Eloi, Montpellier, 34000, France
| | - Sylvie Mallié
- Institute for Neurosciences of Montpellier, INSERM, Institut National de la Santé et de la Recherche Médicale, UMR1051, Hôpital Saint-Eloi, Montpellier, 34000, France.,Université de Montpellier, Montpellier, 34000, France
| | - Antoine Jouvenel
- Institute for Neurosciences of Montpellier, INSERM, Institut National de la Santé et de la Recherche Médicale, UMR1051, Hôpital Saint-Eloi, Montpellier, 34000, France.,Université de Montpellier, Montpellier, 34000, France
| | - Adrien Tassou
- Institute for Neurosciences of Montpellier, INSERM, Institut National de la Santé et de la Recherche Médicale, UMR1051, Hôpital Saint-Eloi, Montpellier, 34000, France.,Université de Montpellier, Montpellier, 34000, France
| | - Henri Haton
- Institute for Neurosciences of Montpellier, INSERM, Institut National de la Santé et de la Recherche Médicale, UMR1051, Hôpital Saint-Eloi, Montpellier, 34000, France.,Université de Montpellier, Montpellier, 34000, France
| | - Stéphanie Venteo
- Institute for Neurosciences of Montpellier, INSERM, Institut National de la Santé et de la Recherche Médicale, UMR1051, Hôpital Saint-Eloi, Montpellier, 34000, France
| | - Jean-Philippe Pin
- Institut de Génomique Fonctionnelle, CNRS, INSERM, Univ. Montpellier, 34094, Montpellier, France
| | - Eric Trinquet
- Cisbio Bioassays, Parc Marcel Boiteux, BP84175, 30200, Codolet, France
| | | | - Alexandre Mezghrani
- Institute for Neurosciences of Montpellier, INSERM, Institut National de la Santé et de la Recherche Médicale, UMR1051, Hôpital Saint-Eloi, Montpellier, 34000, France
| | - Willy Joly
- Institute for Neurosciences of Montpellier, INSERM, Institut National de la Santé et de la Recherche Médicale, UMR1051, Hôpital Saint-Eloi, Montpellier, 34000, France
| | - Julie Mion
- Institute for Neurosciences of Montpellier, INSERM, Institut National de la Santé et de la Recherche Médicale, UMR1051, Hôpital Saint-Eloi, Montpellier, 34000, France
| | - Martine Schmitt
- Laboratoire d'Innovation Thérapeutique, UMR7200, CNRS-Université de Strasbourg, Illkirch, 67400, France
| | - Alexandre Pattyn
- Institute for Neurosciences of Montpellier, INSERM, Institut National de la Santé et de la Recherche Médicale, UMR1051, Hôpital Saint-Eloi, Montpellier, 34000, France
| | - Frédéric Marmigère
- Institute for Neurosciences of Montpellier, INSERM, Institut National de la Santé et de la Recherche Médicale, UMR1051, Hôpital Saint-Eloi, Montpellier, 34000, France
| | | | - Patrick Carroll
- Institute for Neurosciences of Montpellier, INSERM, Institut National de la Santé et de la Recherche Médicale, UMR1051, Hôpital Saint-Eloi, Montpellier, 34000, France
| | - Didier Rognan
- Laboratoire d'Innovation Thérapeutique, UMR7200, CNRS-Université de Strasbourg, Illkirch, 67400, France.
| | - Jean Valmier
- Institute for Neurosciences of Montpellier, INSERM, Institut National de la Santé et de la Recherche Médicale, UMR1051, Hôpital Saint-Eloi, Montpellier, 34000, France. .,Université de Montpellier, Montpellier, 34000, France.
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Lu S, Ji M, Ni D, Zhang J. Discovery of hidden allosteric sites as novel targets for allosteric drug design. Drug Discov Today 2018; 23:359-365. [DOI: 10.1016/j.drudis.2017.10.001] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2017] [Revised: 09/27/2017] [Accepted: 10/05/2017] [Indexed: 02/07/2023]
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38
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Allosteric Modulation of Intact γ-Secretase Structural Dynamics. Biophys J 2018; 113:2634-2649. [PMID: 29262358 DOI: 10.1016/j.bpj.2017.10.012] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 09/26/2017] [Accepted: 10/10/2017] [Indexed: 12/20/2022] Open
Abstract
As a protease complex involved in the cleavage of amyloid precursor proteins that lead to the formation of amyloid β fibrils implicated in Alzheimer's disease, γ-secretase is an important target for developing therapeutics against Alzheimer's disease. γ-secretase is composed of four subunits: nicastrin (NCT) in the extracellular (EC) domain, presenilin-1 (PS1), anterior pharynx defective 1, and presenilin enhancer 2 in the transmembrane (TM) domain. NCT and PS1 play important roles in binding amyloid β precursor proteins and modulating PS1 catalytic activity. Yet, the molecular mechanisms of coupling between substrate/modulator binding and catalytic activity remain to be elucidated. Recent determination of intact human γ-secretase cryo-electron microscopy structure has opened the way for a detailed investigation of the structural dynamics of this complex. Our analysis, based on a membrane-coupled anisotropic network model, reveals two types of NCT motions, bending and twisting, with respect to PS1. These underlie the fluctuations between the "open" and "closed" states of the lid-like NCT with respect to a hydrophilic loop 1 (HL1) on PS1, thus allowing or blocking access of the substrate peptide (EC portion) to HL1 and to the neighboring helix TM2. In addition to this alternating access mechanism, fluctuations in the volume of the PS1 central cavity facilitate the exposure of the catalytic site for substrate cleavage. Druggability simulations show that γ-secretase presents several hot spots for either orthosteric or allosteric inhibition of catalytic activity, consistent with experimental data. In particular, a hinge region at the interface between the EC and TM domains, near the interlobe groove of NCT, emerges as an allo-targeting site that would impact the coupling between HL1/TM2 and the catalytic pocket, opening, to our knowledge, new avenues for structure-based design of novel allosteric modulators of γ-secretase protease activity.
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Abstract
An orthosteric site is commonly viewed as the primary, functionally binding pocket on a receptor. Signal molecules, endogenous agonists, and substrates are recognized by and bind to the orthosteric site of a specific target, resulting in a biological effect. A malfunctioning active site on a crucial receptor has been confirmed as the culprit that causes many metabolic disturbances, neurologic disorders, and genetic diseases. A competitive inhibitor that has a stronger binding affinity can outcompete an orthosteric ligand. An allosteric site, which is nonoverlapping and topographically distinct from the active pocket, can emerge as a potential regulatory site on the protein surface. An allosteric modulator interacts with a specific binding site, affecting the atoms of nearby residues, thus eliciting a series of conformational changes in the residues at the active site through propagation pathways. Allosteric regulation can potentiate or inhibit function instead of blocking it, and this is a promising strategy for drug design. In this chapter, we describe the tools and protocols for allosteric site analysis and allosteric ligand design.
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Affiliation(s)
- Kun Song
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education, Shanghai Jiao-Tong University School of Medicine, Shanghai, China
| | - Jian Zhang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education, Shanghai Jiao-Tong University School of Medicine, Shanghai, China.
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40
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Abraham MM, Denton RE, Harper RW, Scott WL, O’Donnell MJ, Durrant JD. Documenting and harnessing the biological potential of molecules in Distributed Drug Discovery (D3) virtual catalogs. Chem Biol Drug Des 2017; 90:909-918. [PMID: 28453915 PMCID: PMC6544362 DOI: 10.1111/cbdd.13012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 04/22/2017] [Accepted: 04/08/2017] [Indexed: 12/16/2022]
Abstract
Virtual molecular catalogs have limited utility if member compounds are (i) difficult to synthesize or (ii) unlikely to have biological activity. The Distributed Drug Discovery (D3) program addresses the synthesis challenge by providing scientists with a free virtual D3 catalog of 73,024 easy-to-synthesize N-acyl unnatural α-amino acids, their methyl esters, and primary amides. The remaining challenge is to document and exploit the bioactivity potential of these compounds. In the current work, a search process is described that retrospectively identifies all virtual D3 compounds classified as bioactive hits in PubChem-cataloged experimental assays. The results provide insight into the broad range of drug-target classes amenable to inhibition and/or agonism by D3-accessible molecules. To encourage computer-aided drug discovery centered on these compounds, a publicly available virtual database of D3 molecules prepared for use with popular computer docking programs is also presented.
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Affiliation(s)
- Milata M. Abraham
- Department of Chemistry and Chemical Biology, Indiana University Purdue University Indianapolis, Indianapolis, Indiana 46202, United States
| | - Ryan E. Denton
- Department of Chemistry and Chemical Biology, Indiana University Purdue University Indianapolis, Indianapolis, Indiana 46202, United States
| | - Richard W. Harper
- Department of Chemistry and Chemical Biology, Indiana University Purdue University Indianapolis, Indianapolis, Indiana 46202, United States
| | - William L. Scott
- Department of Chemistry and Chemical Biology, Indiana University Purdue University Indianapolis, Indianapolis, Indiana 46202, United States
| | - Martin J. O’Donnell
- Department of Chemistry and Chemical Biology, Indiana University Purdue University Indianapolis, Indianapolis, Indiana 46202, United States
| | - Jacob D. Durrant
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, 15260, United States
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41
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Huang C, Liu Y, Beenken A, Jiang L, Gao X, Huang Z, Hsu A, Gross GJ, Wang YG, Mohammadi M, Schultz JEJ. A novel fibroblast growth factor-1 ligand with reduced heparin binding protects the heart against ischemia-reperfusion injury in the presence of heparin co-administration. Cardiovasc Res 2017; 113:1585-1602. [PMID: 29016740 PMCID: PMC5852627 DOI: 10.1093/cvr/cvx165] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 03/20/2017] [Accepted: 08/10/2017] [Indexed: 12/12/2022] Open
Abstract
AIMS Fibroblast growth factor 1 (FGF1), a heparin/heparan sulfate-binding growth factor, is a potent cardioprotective agent against myocardial infarction (MI). The impact of heparin, the standard of care for MI patients entering the emergency room, on cardioprotective effects of FGF1 is unknown, however. METHODS AND RESULTS To address this, a rat model of MI was employed to compare cardioprotective potentials (lower infarct size and improve post-ischemic function) of native FGF1 and an engineered FGF1 (FGF1ΔHBS) with reduced heparin-binding affinity when given at the onset of reperfusion in the absence or presence of heparin. FGF1 and FGF1ΔHBS did not alter heparin's anticoagulant properties. Treatment with heparin alone or native FGF1 significantly reduced infarct size compared to saline (P < 0.05). Surprisingly, treatment with FGF1ΔHBS markedly lowered infarct size compared to FGF1 (P < 0.05). Both native and modified FGF1 restored contractile and relaxation function (P < 0.05 versus saline or heparin). Furthermore, FGF1ΔHBS had greater improvement in cardiac function compared to FGF1 (P < 0.05). Heparin negatively impacted the cardioprotective effects (infarct size, post-ischemic recovery of function) of FGF1 (P < 0.05) but not of FGF1ΔHBS. Heparin also reduced the biodistribution of FGF1, but not FGF1ΔHBS, to the left ventricle. FGF1 and FGF1ΔHBS bound and triggered FGFR1-induced downstream activation of ERK1/2 (P < 0.05); yet, heparin co-treatment decreased FGF1-produced ERK1/2 activation, but not that activated by FGF1ΔHBS. CONCLUSION These findings demonstrate that modification of the heparin-binding region of FGF1 significantly improves the cardioprotective efficacy, even in the presence of heparin, identifying a novel FGF ligand available for therapeutic use in ischemic heart disease.
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Affiliation(s)
- Chahua Huang
- Department of Pharmacology and Cell Biophysics, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
- Department of Cardiology, Second Affiliated Hospital, Nanchang University, Nanchang 330006, China
| | - Yang Liu
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Andrew Beenken
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Lin Jiang
- Department of Pathology and Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Xiang Gao
- Department of Pathology and Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Zhifeng Huang
- School of Pharmacy and Center for Structural Biology, Wenzhou Medical University, Zhejiang 325035, China
| | - Anna Hsu
- Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Garrett J. Gross
- Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Yi-Gang Wang
- Department of Pathology and Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Moosa Mohammadi
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Jo El J. Schultz
- Department of Pharmacology and Cell Biophysics, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
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42
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Changeux JP, Christopoulos A. Allosteric modulation as a unifying mechanism for receptor function and regulation. Diabetes Obes Metab 2017; 19 Suppl 1:4-21. [PMID: 28880476 DOI: 10.1111/dom.12959] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Four major receptor families enable cells to respond to chemical and physical signals from their proximal environment. The ligand- and voltage-gated ion channels, G-protein-coupled receptors, nuclear hormone receptors and receptor tyrosine kinases are all allosteric proteins that carry multiple, spatially distinct, yet conformationally linked ligand-binding sites. Recent studies point to common mechanisms governing the allosteric transitions of these receptors, including the impact of oligomerization, pre-existing and functionally distinct conformational ensembles, intrinsically disordered regions, and the occurrence of allosteric modulatory sites. Importantly, synthetic allosteric modulators are being discovered for these receptors, providing an enriched, yet challenging, landscape for novel therapeutics.
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MESH Headings
- Allosteric Regulation/drug effects
- Allosteric Site/drug effects
- Animals
- Binding Sites/drug effects
- Dimerization
- Drug Discovery/trends
- Drugs, Investigational/chemistry
- Drugs, Investigational/pharmacology
- Humans
- Ligand-Gated Ion Channels/agonists
- Ligand-Gated Ion Channels/antagonists & inhibitors
- Ligand-Gated Ion Channels/chemistry
- Ligand-Gated Ion Channels/metabolism
- Ligands
- Models, Molecular
- Protein Conformation/drug effects
- Protein Multimerization/drug effects
- Receptor Protein-Tyrosine Kinases/agonists
- Receptor Protein-Tyrosine Kinases/antagonists & inhibitors
- Receptor Protein-Tyrosine Kinases/chemistry
- Receptor Protein-Tyrosine Kinases/metabolism
- Receptors, Cytoplasmic and Nuclear/agonists
- Receptors, Cytoplasmic and Nuclear/antagonists & inhibitors
- Receptors, Cytoplasmic and Nuclear/chemistry
- Receptors, Cytoplasmic and Nuclear/metabolism
- Receptors, G-Protein-Coupled/agonists
- Receptors, G-Protein-Coupled/antagonists & inhibitors
- Receptors, G-Protein-Coupled/chemistry
- Receptors, G-Protein-Coupled/metabolism
- Voltage-Gated Sodium Channels/chemistry
- Voltage-Gated Sodium Channels/metabolism
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Affiliation(s)
| | - Arthur Christopoulos
- Drug Discovery Biology and Department of Pharmacology, Monash Institute of Pharmaceutical Sciences, Monash University, VIC 3052 Parkville, Australia
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Xiao Y, Shaw GS, Konermann L. Calcium-Mediated Control of S100 Proteins: Allosteric Communication via an Agitator/Signal Blocking Mechanism. J Am Chem Soc 2017; 139:11460-11470. [PMID: 28758397 DOI: 10.1021/jacs.7b04380] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Allosteric proteins possess dynamically coupled residues for the propagation of input signals to distant target binding sites. The input signals usually correspond to "effector is present" or "effector is not present". Many aspects of allosteric regulation remain incompletely understood. This work focused on S100A11, a dimeric EF-hand protein with two hydrophobic target binding sites. An annexin peptide (Ax) served as the target. Target binding is allosterically controlled by Ca2+ over a distance of ∼26 Å. Ca2+ promotes formation of a [Ca4 S100 Ax2] complex, where the Ax peptides are accommodated between helices III/IV and III'/IV'. Without Ca2+ these binding sites are closed, precluding interactions with Ax. The allosteric mechanism was probed by microsecond MD simulations in explicit water, complemented by hydrogen exchange mass spectrometry (HDX/MS). Consistent with experimental data, MD runs in the absence of Ca2+ and Ax culminated in target binding site closure. In simulations on [Ca4 S100] the target binding sites remained open. These results capture the essence of allosteric control, revealing how Ca2+ prevents binding site closure. Both HDX/MS and MD data showed that the metalation sites become more dynamic after Ca2+ loss. However, these enhanced dynamics do not represent the primary trigger of the allosteric cascade. Instead, a labile salt bridge acts as an incessantly active "agitator" that destabilizes the packing of adjacent residues, causing a domino chain of events that culminates in target binding site closure. This agitator represents the starting point of the allosteric signal propagation pathway. Ca2+ binding rigidifies elements along this pathway, thereby blocking signal transmission. This blocking mechanism does not conform to the commonly held view that allosteric communication pathways generally originate at the sites where effectors interact with the protein.
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Affiliation(s)
- Yiming Xiao
- Department of Chemistry, The University of Western Ontario , London, Ontario N6A 5B7, Canada
| | - Gary S Shaw
- Department of Chemistry, The University of Western Ontario , London, Ontario N6A 5B7, Canada
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario , London, Ontario N6A 5B7, Canada
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Amin J, Subbarayan MS. Orthosteric- versus allosteric-dependent activation of the GABA A receptor requires numerically distinct subunit level rearrangements. Sci Rep 2017; 7:7770. [PMID: 28798394 PMCID: PMC5552871 DOI: 10.1038/s41598-017-08031-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 07/07/2017] [Indexed: 12/05/2022] Open
Abstract
Anaesthetic molecules act on synaptic transmission via the allosteric modulation of ligand-gated chloride channels, such as hetero-oligomeric α1β2γ2 GABAA receptors. To elucidate the overall activation paradigm via allosteric versus orthosteric sites, we used highly homologous, but homo-oligomeric, ρ1 receptors that are contrastingly insensitive to anaesthetics and respond partially to several full GABA α1β2γ2 receptor agonists. Here, we coexpressed varying ratios of RNAs encoding the wild-type and the mutated ρ1 subunits, which are anaesthetic-sensitive and respond with full efficacy to partial GABA agonists, to generate distinct ensembles of receptors containing five, four, three, two, one, or zero mutated subunits. Using these experiments, we then demonstrate that, in the pentamer, three anaesthetic-sensitive ρ1 subunits are needed to impart full efficacy to the partial GABA agonists. By contrast, five anaesthetic-sensitive subunits are required for direct activation by anaesthetics alone, and only one anaesthetic-sensitive subunit is sufficient to confer the anaesthetic-dependent potentiation to the GABA current. In conclusion, our data indicate that GABA and anaesthetics holistically activate the GABAA ρ1 receptor through distinct subunit level rearrangements and suggest that in contrast to the global impact of GABA via orthosteric sites, the force of anaesthetics through allosteric sites may not propagate to the neighbouring subunits and, thus, may have only a local and limited effect on the ρ1 GABAA receptor model system.
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Affiliation(s)
- Jahanshah Amin
- Department of Molecular Pharmacology and Physiology, Morsani College of Medicine, University of South Florida, Tampa, Florida, 33612, USA.
| | - Meena S Subbarayan
- Department of Molecular Pharmacology and Physiology, Morsani College of Medicine, University of South Florida, Tampa, Florida, 33612, USA
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45
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The long-term effects of stress and kappa opioid receptor activation on conditioned place aversion in male and female California mice. Behav Brain Res 2017. [PMID: 28625549 DOI: 10.1016/j.bbr.2017.06.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Psychosocial stress leads to the activation of kappa opioid receptors (KORs), which induce dysphoria and facilitate depression-like behaviors. However, less is known about the long-term effects of stress and KORs in females. We examined the long-term effects of social defeat stress on the aversive properties of KOR activation in male and female California mice (Peromyscus californicus) using a conditioned place aversion paradigm. Female California mice naïve to social defeat, formed a place aversion following treatment with 2.5mg/kg of the KOR agonist U50,488, but females exposed to defeat did not form a place aversion to this dose. This supports the finding by others that social defeat weakens the aversive properties of KOR agonists. In contrast, both control and stressed males formed an aversion to 10mg/kg of U50,488. We also examined EGR1 immunoreactivity, an indirect marker of neuronal activity, in the nucleus accumbens (NAc) and found that stress and treatment with 10mg/kg of U50,488 increased EGR1 immunoreactivity in the NAc core in females but reduced activation in males. The effects of stress and U50,488 on EGR1 were specific to the NAc, as we found no differences in the bed nucleus of the stria terminalis. In summary, our data indicate important sex differences in the long-term effects of stress and indicate the need for further study of the molecular mechanisms mediating the behavioral effects of KOR in both males and females.
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Copani A. The underexplored question of β-amyloid monomers. Eur J Pharmacol 2017; 817:71-75. [PMID: 28577967 DOI: 10.1016/j.ejphar.2017.05.057] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 05/12/2017] [Accepted: 05/30/2017] [Indexed: 01/03/2023]
Abstract
Conceived more than 25 years ago, the amyloid cascade hypothesis of Alzheimer's disease has evolved to accommodate new findings, namely different forms of β-amyloid aggregates and downstream dysfunctions. Yet, the cascade does not mention its very beginning, the β-amyloid monomer. Here, I will discuss the monomer from a functional evolutionary perspective, highlighting the potential advantages of a native unfolded state that, however, involves an amyloidogenic risk. Finally, I will make a summary of what is known about its functional role in the brain and discuss the implications of its conceivable shortage in the development of Alzheimer's disease.
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Affiliation(s)
- Agata Copani
- Department of Drug Sciences, University of Catania, Viale Andrea Doria 6, 95125 Catania, Italy.
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Yang Y, Yu Y, Li X, Li J, Wu Y, Yu J, Ge J, Huang Z, Jiang L, Rao Y, Yang M. Target Elucidation by Cocrystal Structures of NADH-Ubiquinone Oxidoreductase of Plasmodium falciparum (PfNDH2) with Small Molecule To Eliminate Drug-Resistant Malaria. J Med Chem 2017; 60:1994-2005. [DOI: 10.1021/acs.jmedchem.6b01733] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Yiqing Yang
- MOE
Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
- MOE
Key Laboratory of Protein Sciences, Tsinghua-Peking Center for Life
Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - You Yu
- MOE
Key Laboratory of Protein Sciences, Tsinghua-Peking Center for Life
Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiaolu Li
- Department
of Biochemistry and Molecular Biology, State Key Laboratory of Medical
Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100005, China
| | - Jing Li
- MOE
Key Laboratory of Protein Sciences, Tsinghua-Peking Center for Life
Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yue Wu
- MOE
Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Jie Yu
- MOE
Key Laboratory of Protein Sciences, Tsinghua-Peking Center for Life
Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jingpeng Ge
- MOE
Key Laboratory of Protein Sciences, Tsinghua-Peking Center for Life
Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zhenghui Huang
- Institut Pasteur of Shanghai, CAS Key Laboratory of Molecular Virology and Immunology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Lubin Jiang
- Institut Pasteur of Shanghai, CAS Key Laboratory of Molecular Virology and Immunology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yu Rao
- MOE
Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Maojun Yang
- MOE
Key Laboratory of Protein Sciences, Tsinghua-Peking Center for Life
Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
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Hanold LE, Fulton MD, Kennedy EJ. Targeting kinase signaling pathways with constrained peptide scaffolds. Pharmacol Ther 2017; 173:159-170. [PMID: 28185915 DOI: 10.1016/j.pharmthera.2017.02.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Kinases are amongst the largest families in the human proteome and serve as critical mediators of a myriad of cell signaling pathways. Since altered kinase activity is implicated in a variety of pathological diseases, kinases have become a prominent class of proteins for targeted inhibition. Although numerous small molecule and antibody-based inhibitors have already received clinical approval, several challenges may still exist with these strategies including resistance, target selection, inhibitor potency and in vivo activity profiles. Constrained peptide inhibitors have emerged as an alternative strategy for kinase inhibition. Distinct from small molecule inhibitors, peptides can provide a large binding surface area that allows them to bind shallow protein surfaces rather than defined pockets within the target protein structure. By including chemical constraints within the peptide sequence, additional benefits can be bestowed onto the peptide scaffold such as improved target affinity and target selectivity, cell permeability and proteolytic resistance. In this review, we highlight examples of diverse chemistries that are being employed to constrain kinase-targeting peptide scaffolds and highlight their application to modulate kinase signaling as well as their potential clinical implications.
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Affiliation(s)
- Laura E Hanold
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA 30602, United States
| | - Melody D Fulton
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA 30602, United States
| | - Eileen J Kennedy
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA 30602, United States.
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Lu S, Zhang J. Designed covalent allosteric modulators: an emerging paradigm in drug discovery. Drug Discov Today 2017; 22:447-453. [DOI: 10.1016/j.drudis.2016.11.013] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 10/04/2016] [Accepted: 11/15/2016] [Indexed: 12/11/2022]
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50
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Scholler P, Moreno-Delgado D, Lecat-Guillet N, Doumazane E, Monnier C, Charrier-Savournin F, Fabre L, Chouvet C, Soldevila S, Lamarque L, Donsimoni G, Roux T, Zwier JM, Trinquet E, Rondard P, Pin JP. HTS-compatible FRET-based conformational sensors clarify membrane receptor activation. Nat Chem Biol 2017; 13:372-380. [DOI: 10.1038/nchembio.2286] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 11/18/2016] [Indexed: 12/26/2022]
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