1
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Khylyuk D. Protein-Protein Docking Approach to GPCR Oligomerization. Methods Mol Biol 2024; 2780:281-287. [PMID: 38987473 DOI: 10.1007/978-1-0716-3985-6_14] [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] [Indexed: 07/12/2024]
Abstract
G-protein-coupled receptors (GPCRs), the largest family of human membrane proteins, play a crucial role in cellular control and are the target of approximately one-third of all drugs on the market. Targeting these complexes with selectivity or formulating small molecules capable of modulating receptor-receptor interactions could potentially offer novel avenues for drug discovery, fostering the development of more refined and safer pharmacotherapies. Due to the lack of experimentally derived X-ray crystallography spectra of GPCR oligomers, there is growing evidence supporting the development of new in silico approaches for predicting GPCR self-assembling structures. The significance of GPCR oligomerization, the challenges in modeling these structures, and the potential of protein-protein docking algorithms to address these challenges are discussed. The study also underscores the use of various software solutions for modeling GPCR oligomeric structures and presents practical cases where these techniques have been successfully applied.
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Affiliation(s)
- Dmytro Khylyuk
- Chair and Department of Organic Chemistry , Medical University of Lublin, Lublin, Poland.
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2
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Zha J, He J, Wu C, Zhang M, Liu X, Zhang J. Designing drugs and chemical probes with the dualsteric approach. Chem Soc Rev 2023; 52:8651-8677. [PMID: 37990599 DOI: 10.1039/d3cs00650f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023]
Abstract
Traditionally, drugs are monovalent, targeting only one site on the protein surface. This includes orthosteric and allosteric drugs, which bind the protein at orthosteric and allosteric sites, respectively. Orthosteric drugs are good in potency, whereas allosteric drugs have better selectivity and are solutions to classically undruggable targets. However, it would be difficult to simultaneously reach high potency and selectivity when targeting only one site. Also, both kinds of monovalent drugs suffer from mutation-caused drug resistance. To overcome these obstacles, dualsteric modulators have been proposed in the past twenty years. Compared to orthosteric or allosteric drugs, dualsteric modulators are bivalent (or bitopic) with two pharmacophores. Each of the two pharmacophores bind the protein at the orthosteric and an allosteric site, which could bring the modulator with special properties beyond monovalent drugs. In this study, we comprehensively review the current development of dualsteric modulators. Our main effort reason and illustrate the aims to apply the dualsteric approach, including a "double win" of potency and selectivity, overcoming mutation-caused drug resistance, developments of function-biased modulators, and design of partial agonists. Moreover, the strengths of the dualsteric technique also led to its application outside pharmacy, including the design of highly sensitive fluorescent tracers and usage as molecular rulers. Besides, we also introduced drug targets, designing strategies, and validation methods of dualsteric modulators. Finally, we detail the conclusions and perspectives.
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Affiliation(s)
- Jinyin Zha
- College of Pharmacy, Ningxia Medical University, Yinchuan, Ningxia Hui Autonomous Region, China.
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jixiao He
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chengwei Wu
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Mingyang Zhang
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xinyi Liu
- College of Pharmacy, Ningxia Medical University, Yinchuan, Ningxia Hui Autonomous Region, China.
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jian Zhang
- College of Pharmacy, Ningxia Medical University, Yinchuan, Ningxia Hui Autonomous Region, China.
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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3
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Weerasinghe DK, Hodge JM, Pasco JA, Samarasinghe RM, Azimi Manavi B, Williams LJ. Antipsychotic-induced bone loss: the role of dopamine, serotonin and adrenergic receptor signalling. Front Cell Dev Biol 2023; 11:1184550. [PMID: 37305679 PMCID: PMC10248006 DOI: 10.3389/fcell.2023.1184550] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 05/09/2023] [Indexed: 06/13/2023] Open
Abstract
Antipsychotics are commonly used in treating psychiatric disorders. These medications primarily target dopamine the serotonin receptors, they have some affinity to adrenergic, histamine, glutamate and muscarinic receptors. There is clinical evidence that antipsychotic use decreases BMD and increases fracture risk, with dopamine, serotonin and adrenergic receptor-signalling becoming an increasing area of focus where the presence of these receptors in osteoclasts and osteoblasts have been demonstrated. Osteoclasts and osteoblasts are the most important cells in the bone remodelling and the bone regeneration process where the activity of these cells determine the bone resorption and formation process in order to maintain healthy bone. However, an imbalance in osteoclast and osteoblast activity can lead to decreased BMD and increased fracture risk, which is also believed to be exacerbated by antipsychotics use. Therefore, the aim of this review is to provide an overview of the mechanisms of action of first, second and third generation antipsychotics and the expression profiles of dopamine, serotonin and adrenergic receptors during osteoclastogenesis and osteoblastogenesis.
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Affiliation(s)
- D. Kavindi Weerasinghe
- IMPACT—The Institute for Mental and Physical Health and Clinical Translation, Deakin University, Geelong, VIC, Australia
| | - Jason M. Hodge
- IMPACT—The Institute for Mental and Physical Health and Clinical Translation, Deakin University, Geelong, VIC, Australia
- Barwon Health, Geelong, VIC, Australia
| | - Julie A. Pasco
- IMPACT—The Institute for Mental and Physical Health and Clinical Translation, Deakin University, Geelong, VIC, Australia
- Barwon Health, Geelong, VIC, Australia
- Department of Medicine—Western Health, The University of Melbourne, Melbourne, VIC, Australia
| | - Rasika M. Samarasinghe
- IMPACT—The Institute for Mental and Physical Health and Clinical Translation, Deakin University, Geelong, VIC, Australia
| | - Behnaz Azimi Manavi
- IMPACT—The Institute for Mental and Physical Health and Clinical Translation, Deakin University, Geelong, VIC, Australia
| | - Lana J. Williams
- IMPACT—The Institute for Mental and Physical Health and Clinical Translation, Deakin University, Geelong, VIC, Australia
- Barwon Health, Geelong, VIC, Australia
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4
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Zell L, Bretl A, Temml V, Schuster D. Dopamine Receptor Ligand Selectivity-An In Silico/In Vitro Insight. Biomedicines 2023; 11:1468. [PMID: 37239139 PMCID: PMC10216180 DOI: 10.3390/biomedicines11051468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/03/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023] Open
Abstract
Different dopamine receptor (DR) subtypes are involved in pathophysiological conditions such as Parkinson's Disease (PD), schizophrenia and depression. While many DR-targeting drugs have been approved by the U.S. Food and Drug Administration (FDA), only a very small number are truly selective for one of the DR subtypes. Additionally, most of them show promiscuous activity at related G-protein coupled receptors, thus suffering from diverse side-effect profiles. Multiple studies have shown that combined in silico/in vitro approaches are a valuable contribution to drug discovery processes. They can also be applied to divulge the mechanisms behind ligand selectivity. In this study, novel DR ligands were investigated in vitro to assess binding affinities at different DR subtypes. Thus, nine D2R/D3R-selective ligands (micro- to nanomolar binding affinities, D3R-selective profile) were successfully identified. The most promising ligand exerted nanomolar D3R activity (Ki = 2.3 nM) with 263.7-fold D2R/D3R selectivity. Subsequently, ligand selectivity was rationalized in silico based on ligand interaction with a secondary binding pocket, supporting the selectivity data determined in vitro. The developed workflow and identified ligands could aid in the further understanding of the structural motifs responsible for DR subtype selectivity, thus benefitting drug development in D2R/D3R-associated pathologies such as PD.
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Affiliation(s)
| | | | | | - Daniela Schuster
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Paracelsus Medical University, 5020 Salzburg, Austria; (L.Z.); (A.B.); (V.T.)
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5
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Sharma S, Monga Y, Gupta A, Singh S. 2-Oxindole and related heterocycles: synthetic methodologies for their natural products and related derivatives. RSC Adv 2023; 13:14249-14267. [PMID: 37179999 PMCID: PMC10173257 DOI: 10.1039/d3ra02217j] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023] Open
Abstract
Natural goods, medications, and pharmaceutically active substances all contain substituted oxindoles. Generally, the C-3 stereocenter of the substituents of oxindoles and their absolute arrangement have a substantial impact on the bioactivity of these substances. In this case, the desire for contemporary probe and drug-discovery programs for the synthesis of chiral compounds using desirable scaffolds with high structural diversity further drives research in this field. Also, the new synthetic techniques are generally simple to apply for the synthesis of other similar scaffolds. Herein, we review the distinct approaches for the synthesis of diverse useful oxindole scaffolds. Specifically, the research findings on the naturally existing 2-oxindole core and a variety of synthetic compounds having a 2-oxindole core are discussed. We present an overview of the construction of oxindole-based synthetic and natural products. In addition, the chemical reactivity of 2-oxindole and its related derivatives in the presence of chiral and achiral catalysts are thoroughly discussed. The data compiled herein provides broad information related to the bioactive product design, development, and applications of 2-oxindoles and the reported techniques will be helpful for the investigation of novel reactions in the future.
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Affiliation(s)
- Shivangi Sharma
- Department of Applied Chemistry, Amity School of Engineering and Technology, Amity University Madhya Pradesh Gwalior Madhya Pradesh-474 005 India
| | - Yukti Monga
- Shyamlal College, Department of Chemistry, University of Delhi Delhi-110032 India
| | - Ashu Gupta
- Shyamlal College, Department of Chemistry, University of Delhi Delhi-110032 India
| | - Shivendra Singh
- Department of Applied Chemistry, Amity School of Engineering and Technology, Amity University Madhya Pradesh Gwalior Madhya Pradesh-474 005 India
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6
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Juza R, Musilek K, Mezeiova E, Soukup O, Korabecny J. Recent advances in dopamine D 2 receptor ligands in the treatment of neuropsychiatric disorders. Med Res Rev 2023; 43:55-211. [PMID: 36111795 DOI: 10.1002/med.21923] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 07/29/2022] [Accepted: 08/09/2022] [Indexed: 02/04/2023]
Abstract
Dopamine is a biologically active amine synthesized in the central and peripheral nervous system. This biogenic monoamine acts by activating five types of dopamine receptors (D1-5 Rs), which belong to the G protein-coupled receptor family. Antagonists and partial agonists of D2 Rs are used to treat schizophrenia, Parkinson's disease, depression, and anxiety. The typical pharmacophore with high D2 R affinity comprises four main areas, namely aromatic moiety, cyclic amine, central linker and aromatic/heteroaromatic lipophilic fragment. From the literature reviewed herein, we can conclude that 4-(2,3-dichlorophenyl), 4-(2-methoxyphenyl)-, 4-(benzo[b]thiophen-4-yl)-1-substituted piperazine, and 4-(6-fluorobenzo[d]isoxazol-3-yl)piperidine moieties are critical for high D2 R affinity. Four to six atoms chains are optimal for D2 R affinity with 4-butoxyl as the most pronounced one. The bicyclic aromatic/heteroaromatic systems are most frequently occurring as lipophilic appendages to retain high D2 R affinity. In this review, we provide a thorough overview of the therapeutic potential of D2 R modulators in the treatment of the aforementioned disorders. In addition, this review summarizes current knowledge about these diseases, with a focus on the dopaminergic pathway underlying these pathologies. Major attention is paid to the structure, function, and pharmacology of novel D2 R ligands, which have been developed in the last decade (2010-2021), and belong to the 1,4-disubstituted aromatic cyclic amine group. Due to the abundance of data, allosteric D2 R ligands and D2 R modulators from patents are not discussed in this review.
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Affiliation(s)
- Radomir Juza
- Experimental Neurobiology, National Institute of Mental Health, Klecany, Czech Republic.,Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove, Czech Republic
| | - Kamil Musilek
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove, Czech Republic.,Biomedical Research Centre, University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
| | - Eva Mezeiova
- Experimental Neurobiology, National Institute of Mental Health, Klecany, Czech Republic.,Biomedical Research Centre, University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
| | - Ondrej Soukup
- Biomedical Research Centre, University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
| | - Jan Korabecny
- Experimental Neurobiology, National Institute of Mental Health, Klecany, Czech Republic.,Biomedical Research Centre, University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
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7
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Kim S, Doukmak EJ, Flax RG, Gray DJ, Zirimu VN, de Jong E, Steinhardt RC. Developing Photoaffinity Probes for Dopamine Receptor D 2 to Determine Targets of Parkinson's Disease Drugs. ACS Chem Neurosci 2022; 13:3008-3022. [PMID: 36183275 PMCID: PMC9585581 DOI: 10.1021/acschemneuro.2c00544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Dopaminergic pathways control highly consequential aspects of physiology and behavior. One of the most therapeutically important and best-studied receptors in these pathways is dopamine receptor D2 (DRD2). Unfortunately, DRD2 is challenging to study with traditional molecular biological techniques, and most drugs designed to target DRD2 are ligands for many other receptors. Here, we developed probes able to both covalently bind to DRD2 using photoaffinity labeling and provide a chemical handle for detection or affinity purification. These probes behaved like good DRD2 agonists in traditional biochemical assays and were able to perform in chemical-biological assays of cell and receptor labeling. Rat whole brain labeling and affinity enrichment using the probes permitted proteomic analysis of the probes' interacting proteins. Bioinformatic study of the hits revealed that the probes bound noncanonically targeted proteins in Parkinson's disease network as well as the retrograde endocannabinoid signaling, neuronal nitric oxide synthase, muscarinic acetylcholine receptor M1, GABA receptor, and dopamine receptor D1 (DRD1) signaling networks. Follow-up analysis may yield insights into how this pathway relates specifically to Parkinson's disease symptoms or provide new targets for treatments. This work reinforces the notion that the combination of chemical biology and omics-based approaches provides a broad picture of a molecule's "interactome" and may also give insight into the pleiotropy of effects observed for a drug or perhaps indicate new applications.
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Affiliation(s)
- Spencer
T. Kim
- Department
of Chemistry, Syracuse University, Syracuse, New York 13244, United States
| | - Emma J. Doukmak
- Department
of Chemistry, Syracuse University, Syracuse, New York 13244, United States
| | - Raymond G. Flax
- Department
of Chemistry, Syracuse University, Syracuse, New York 13244, United States
| | - Dylan J. Gray
- Department
of Chemistry, Syracuse University, Syracuse, New York 13244, United States
| | - Victoria N. Zirimu
- Department
of Chemistry, Syracuse University, Syracuse, New York 13244, United States
| | - Ebbing de Jong
- SUNY
Upstate Medical University, Syracuse, New York 13244, United States
| | - Rachel C. Steinhardt
- Department
of Chemistry, Syracuse University, Syracuse, New York 13244, United States,BioInspired
Institute, Syracuse University, Syracuse, New York 13244, United States,Department
of Biomedical and Chemical Engineering, Syracuse University, Syracuse, New York 13244, United States,
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8
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Kaczor AA, Wojtunik-Kulesza K, Wróbel TM, Matosiuk D, Pitucha M. 5-Methoxy-1-methyl-2-{[4-(2-hydroxyphenyl)piperazin-1-yl]methyl}-1Hindole (KAD22) with Antioxidant Activity. LETT ORG CHEM 2022. [DOI: 10.2174/1570178618666210119121438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
:
Compound KAD22 (5-methoxy-1-methyl-2-[4-(2-hydroxyphenyl)piperazin-1-yl]methyl-1H-indole) was designed as a potential dopamine D2 receptor agonist with antioxidant activity for possible treatment of Parkinson’s disease.
The compound was obtained from 5-methoxy-1-methyl-1H-indole-2-carbaldehyde and 2-(piperazin-1-yl)phenol. KAD22
showed no affinity to dopamine D2 receptor but it is a potent antioxidant. Experimental and computational structural studies
(conformational analysis, HOMO and LUMO orbitals, electrostatic potential map, non-covalent interaction plot, spectral
properties, ligand-receptor interactions) of KAD22 were performed to address its biological activity.
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Affiliation(s)
- Agnieszka A. Kaczor
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances, Faculty of Pharmacy, Medical
University of Lublin, 4A Chodzki St., PL-20093 Lublin, Poland
| | - Karolina Wojtunik-Kulesza
- Department of Inorganic Chemistry, Faculty of
Pharmacy, Medical University of Lublin, 4A Chodzki St., PL-20093 Lublin, Poland
| | - Tomasz M. Wróbel
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances, Faculty of Pharmacy, Medical
University of Lublin, 4A Chodzki St., PL-20093 Lublin, Poland
| | - Dariusz Matosiuk
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances, Faculty of Pharmacy, Medical
University of Lublin, 4A Chodzki St., PL-20093 Lublin, Poland
| | - Monika Pitucha
- Independent Radiopharmacy Unit,
Department of Organic Chemistry, Faculty of Pharmacy, Medical University of Lublin, 4A Chodzki St., PL-20093
Lublin, Poland
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9
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Khetmalis YM, Shivani M, Murugesan S, Chandra Sekhar KVG. Oxindole and its derivatives: A review on recent progress in biological activities. Biomed Pharmacother 2021; 141:111842. [PMID: 34174506 DOI: 10.1016/j.biopha.2021.111842] [Citation(s) in RCA: 105] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 06/02/2021] [Accepted: 06/16/2021] [Indexed: 12/13/2022] Open
Abstract
Oxindole has been shown to be a pharmacologically advantageous scaffold having many biological properties that are relevant to medicinal chemistry. The simplicity and widespread occurrence of this scaffold in plant-based alkaloids have further reinforced oxindole's merit in the domain of novel drug discovery. First extracted from Uncaria tomentosa, commonly the known as cat claw's plant which was found abundantly in the Amazon rainforest, molecules with the oxindole moiety have been shown to be common in a wide variety of compounds extracted from plant sources. The role of oxindole as a chemical scaffold for fabricating and designing biological drugs agents can be ascribed to its ability to be modified by a number of chemical groups to generate novel biological functions. This review is aimed at providing a description of the general chemistry based on existing corresponding structure-activity relationships (SARs) and compile all recent developmentary studies on oxindole-derived compounds as a successful pharmaceutical agent. A substantial group of oxindole derivatives are chiefly being tested as anticancer agents, however, a several oxindole derivatives have been shown to possesses antimicrobial, α-glucosidase inhibitory, antiviral, antileishmanial, antitubercular, antioxidative, tyrosinase inhibitory, PAK4 inhibitory, antirheumatoid arthritis and intraocular pressure reducing activities, to name a few. In this review we show the potential value of developing newer oxindole derivatives with an improved range of pharmacological implications as well as identifying drugs possessing oxindole core, that are showing and serving increased efficacy in clinical practice.
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Affiliation(s)
- Yogesh Mahadu Khetmalis
- Department of Chemistry, Birla Institute of Technology and Science, Pilani, Hyderabad Campus, Jawahar Nagar, Kapra Mandal, Hyderabad 500078, Telangana, India
| | - Mithula Shivani
- Department of Chemistry, Birla Institute of Technology and Science, Pilani, Hyderabad Campus, Jawahar Nagar, Kapra Mandal, Hyderabad 500078, Telangana, India
| | - Sankaranarayanan Murugesan
- Medicinal Chemistry Research Laboratory, Department of Pharmacy, Birla Institute of Technology and Science Pilani, Pilani Campus, Pilani 33303, Rajasthan, India
| | - Kondapalli Venkata Gowri Chandra Sekhar
- Department of Chemistry, Birla Institute of Technology and Science, Pilani, Hyderabad Campus, Jawahar Nagar, Kapra Mandal, Hyderabad 500078, Telangana, India.
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10
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Ullmann T, Gienger M, Budzinski J, Hellmann J, Hübner H, Gmeiner P, Weikert D. Homobivalent Dopamine D 2 Receptor Ligands Modulate the Dynamic Equilibrium of D 2 Monomers and Homo- and Heterodimers. ACS Chem Biol 2021; 16:371-379. [PMID: 33435665 DOI: 10.1021/acschembio.0c00895] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Dopamine D2 receptors (D2Rs) are major targets in the treatment of psychiatric and neurodegenerative diseases. As with many other G protein-coupled receptors (GPCRs), D2Rs interact within the cellular membrane, leading to a transient receptor homo- or heterodimerization. These interactions are known to alter ligand binding, signaling, and receptor trafficking. Bivalent ligands are ideally suited to target GPCR dimers and are composed of two pharmacophores connected by a spacer element. If properly designed, bivalent ligands are able to engange the two orthosteric binding sites of a GPCR dimer simultaneously. Taking advantage of previously developed ligands for heterodimers of D2R and the neurotensin receptor 1 (NTSR1), we synthesized homobivalent ligands targeting D2R. Employing bioluminescence resonance energy transfer, we found that the bivalent ligands 3b and 4b comprising a 92-atom spacer are able to foster D2R-homodimerization while simultaneously reducing interactions of D2R with NTSR1. Both receptors are coexpressed in the central nervous system and involved in important physiological processes. The newly developed bivalent ligands are excellent tools to further understand the pharmacological consequences of D2R homo- and heterodimerization. Not limited to the dopaminergic system, modifying class A GPCRs' dynamic equilibrium between monomers, homomers, and heteromers with bivalent ligands may represent a novel pharmacological concept paving the way toward innovative drugs.
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Affiliation(s)
- Tamara Ullmann
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, 91058 Erlangen, Germany
| | - Marie Gienger
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, 91058 Erlangen, Germany
| | - Julian Budzinski
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, 91058 Erlangen, Germany
| | - Jan Hellmann
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, 91058 Erlangen, Germany
| | - Harald Hübner
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, 91058 Erlangen, Germany
| | - Peter Gmeiner
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, 91058 Erlangen, Germany
| | - Dorothee Weikert
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, 91058 Erlangen, Germany
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11
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Matera C, Bono F, Pelucchi S, Collo G, Bontempi L, Gotti C, Zoli M, De Amici M, Missale C, Fiorentini C, Dallanoce C. The novel hybrid agonist HyNDA-1 targets the D3R-nAChR heteromeric complex in dopaminergic neurons. Biochem Pharmacol 2019; 163:154-168. [PMID: 30772268 DOI: 10.1016/j.bcp.2019.02.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 02/13/2019] [Indexed: 02/07/2023]
Abstract
In this paper, we designed, synthesized and tested a small set of three new derivatives potentially targeting the D3R-nAChR heteromer, a receptor complex recently identified and characterized as the molecular entity that, in dopaminergic neurons, mediates the neurotrophic effects of nicotine. By means of a partially rigidified spacer of variable length, we incorporated in the new compounds (1a-c) the pharmacophoric substructure of a known β2-subunit-containing nAChR agonist (A-84543) and that of the D2/D3R agonist drug ropinirole. All the compounds retained the ability to bind with high affinity both β2-subunit-containing nAChR and D3R. Compound 1a, renamed HyNDA-1, which is characterized by the shortest linker moiety, was the most interesting ligand. We found, in fact, that HyNDA-1 significantly modulated structural plasticity on both mice and human dopaminergic neurons, an effect strongly prevented by co-incubating this ligand with either nAChR or D3R antagonists. Moreover, the neurotrophic effects of HyNDA-1 were specifically lost by disrupting the complex with specific interfering peptides. Interestingly, by using the Bioluminescence Resonance Energy Transfer 2 (BRET2) assay in HEK-293 transfected cells, we also found that HyNDA-1 has the ability to increase the affinity of interaction between nAChR and D3R. Overall, our results indicate that the neurotrophic effects of HyNDA-1 are mediated by activation of the D3R-nAChR heteromeric complex specifically expressed on dopaminergic neurons.
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Affiliation(s)
- Carlo Matera
- Dipartimento di Scienze Farmaceutiche - Sezione di Chimica Farmaceutica "Pietro Pratesi", Università degli Studi di Milano, Via L. Mangiagalli 25, 20133 Milano, Italy
| | - Federica Bono
- Dipartimento di Medicina Molecolare e Traslazionale - Sezione di Farmacologia, Università degli Studi di Brescia, Viale Europa 11, 25123 Brescia, Italy
| | - Silvia Pelucchi
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti 9, 20133 Milano, Italy
| | - Ginetta Collo
- Dipartimento di Medicina Molecolare e Traslazionale - Sezione di Farmacologia, Università degli Studi di Brescia, Viale Europa 11, 25123 Brescia, Italy
| | - Leonardo Bontempi
- Dipartimento di Medicina Molecolare e Traslazionale - Sezione di Farmacologia, Università degli Studi di Brescia, Viale Europa 11, 25123 Brescia, Italy
| | - Cecilia Gotti
- Istituto di Neuroscienze, CNR, Via Vanvitelli 32, 20129 Milan, Italy
| | - Michele Zoli
- Dipartimento di Scienze Biomediche, Metaboliche e Neuroscienze, Università degli Studi di Modena e Reggio Emilia, Via G. Campi 287, 41125 Modena, Italy
| | - Marco De Amici
- Dipartimento di Scienze Farmaceutiche - Sezione di Chimica Farmaceutica "Pietro Pratesi", Università degli Studi di Milano, Via L. Mangiagalli 25, 20133 Milano, Italy
| | - Cristina Missale
- Dipartimento di Medicina Molecolare e Traslazionale - Sezione di Farmacologia, Università degli Studi di Brescia, Viale Europa 11, 25123 Brescia, Italy
| | - Chiara Fiorentini
- Dipartimento di Medicina Molecolare e Traslazionale - Sezione di Farmacologia, Università degli Studi di Brescia, Viale Europa 11, 25123 Brescia, Italy.
| | - Clelia Dallanoce
- Dipartimento di Scienze Farmaceutiche - Sezione di Chimica Farmaceutica "Pietro Pratesi", Università degli Studi di Milano, Via L. Mangiagalli 25, 20133 Milano, Italy.
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12
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Kaczor AA, Bartuzi D, Stępniewski TM, Matosiuk D, Selent J. Protein-Protein Docking in Drug Design and Discovery. Methods Mol Biol 2019; 1762:285-305. [PMID: 29594778 DOI: 10.1007/978-1-4939-7756-7_15] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Protein-protein interactions (PPIs) are responsible for a number of key physiological processes in the living cells and underlie the pathomechanism of many diseases. Nowadays, along with the concept of so-called "hot spots" in protein-protein interactions, which are well-defined interface regions responsible for most of the binding energy, these interfaces can be targeted with modulators. In order to apply structure-based design techniques to design PPIs modulators, a three-dimensional structure of protein complex has to be available. In this context in silico approaches, in particular protein-protein docking, are a valuable complement to experimental methods for elucidating 3D structure of protein complexes. Protein-protein docking is easy to use and does not require significant computer resources and time (in contrast to molecular dynamics) and it results in 3D structure of a protein complex (in contrast to sequence-based methods of predicting binding interfaces). However, protein-protein docking cannot address all the aspects of protein dynamics, in particular the global conformational changes during protein complex formation. In spite of this fact, protein-protein docking is widely used to model complexes of water-soluble proteins and less commonly to predict structures of transmembrane protein assemblies, including dimers and oligomers of G protein-coupled receptors (GPCRs). In this chapter we review the principles of protein-protein docking, available algorithms and software and discuss the recent examples, benefits, and drawbacks of protein-protein docking application to water-soluble proteins, membrane anchoring and transmembrane proteins, including GPCRs.
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Affiliation(s)
- Agnieszka A Kaczor
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modelling Lab, Medical University of Lublin, Lublin, Poland. .,School of Pharmacy, University of Eastern Finland, Kuopio, Finland.
| | - Damian Bartuzi
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modelling Lab, Medical University of Lublin, Lublin, Poland
| | - Tomasz Maciej Stępniewski
- GPCR Drug Discovery Group, Research Programme on Biomedical Informatics (GRIB), Universitat Pompeu Fabra (UPF)-Hospital del Mar Medical Research Institute (IMIM), Parc de Recerca Biomèdica de Barcelona (PRBB), Barcelona, Spain
| | - Dariusz Matosiuk
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modelling Lab, Medical University of Lublin, Lublin, Poland
| | - Jana Selent
- GPCR Drug Discovery Group, Research Programme on Biomedical Informatics (GRIB), Universitat Pompeu Fabra (UPF)-Hospital del Mar Medical Research Institute (IMIM), Parc de Recerca Biomèdica de Barcelona (PRBB), Barcelona, Spain
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Quadri SAI, Das TC, Jadhav S, Farooqui M. Efficient synthesis of tertiary amine by direct N-alkylation of secondary amine with carboxylic acid using Ni (0) encat catalyst. SYNTHETIC COMMUN 2018. [DOI: 10.1080/00397911.2017.1396613] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
| | - Tonmoy C. Das
- Department of Chemistry, Dr. Rafiq Zakaria College for Women, Aurangabad, India
| | - Shivaji Jadhav
- Department of Chemistry, Dr. Rafiq Zakaria College for Women, Aurangabad, India
| | - Mazahar Farooqui
- Department of Chemistry, Dr. Rafiq Zakaria College for Women, Aurangabad, India
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Gurturk Z, Tezcaner A, Dalgic AD, Korkmaz S, Keskin D. Maltodextrin modified liposomes for drug delivery through the blood-brain barrier. MEDCHEMCOMM 2017; 8:1337-1345. [PMID: 30108846 DOI: 10.1039/c7md00045f] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 05/05/2017] [Indexed: 11/21/2022]
Abstract
Central nervous system acting drugs, when administered intravenously, cannot show their effect in the brain due to the difficulty in crossing the blood-brain barrier (BBB). Levodopa is one of those drugs that are used to treat Parkinson's disease. In this study, a new liposomal levodopa delivery system that is modified with maltodextrin was developed in order to target and enhance transport through the BBB. An antioxidant, glutathione, was co-loaded in liposomes as a supportive agent and its effect on liposome stability and delivery was investigated. Glutathione co-loading had a positive effect on the viabilities of 3T3 and SH-SY5Y cells. Maltodextrin targeted liposomes showed high in vitro levodopa passage in the parallel artificial membrane permeability assay and had superior binding to MDCK cells. Results suggest that maltodextrin modification of liposomes is an effective way of targeting the BBB and the developed liposomal formulation would improve brain delivery of central nervous system agents.
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Affiliation(s)
- Zeynep Gurturk
- Department of Biotechnology , Middle East Technical University , Ankara , 06800 , Turkey .
| | - Aysen Tezcaner
- Department of Biotechnology , Middle East Technical University , Ankara , 06800 , Turkey . .,Department of Engineering Sciences , Middle East Technical University , Ankara , 06800 , Turkey.,BIOMATEN , Center of Excellence in Biomaterials and Tissue Engineering , Middle East Technical University , Ankara , 06800 , Turkey
| | - Ali Deniz Dalgic
- Department of Engineering Sciences , Middle East Technical University , Ankara , 06800 , Turkey
| | - Seval Korkmaz
- Ali Raif Pharmaceutical Corporation , Istanbul , 34555 , Turkey
| | - Dilek Keskin
- Department of Biotechnology , Middle East Technical University , Ankara , 06800 , Turkey . .,Department of Engineering Sciences , Middle East Technical University , Ankara , 06800 , Turkey.,BIOMATEN , Center of Excellence in Biomaterials and Tissue Engineering , Middle East Technical University , Ankara , 06800 , Turkey
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Bartuzi D, Kaczor AA, Targowska-Duda KM, Matosiuk D. Recent Advances and Applications of Molecular Docking to G Protein-Coupled Receptors. Molecules 2017; 22:molecules22020340. [PMID: 28241450 PMCID: PMC6155844 DOI: 10.3390/molecules22020340] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 01/27/2017] [Accepted: 02/15/2017] [Indexed: 12/16/2022] Open
Abstract
The growing number of studies on G protein-coupled receptors (GPCRs) family are a source of noticeable improvement in our understanding of the functioning of these proteins. GPCRs are responsible for a vast part of signaling in vertebrates and, as such, invariably remain in the spotlight of medicinal chemistry. A deeper insight into the underlying mechanisms of interesting phenomena observed in GPCRs, such as biased signaling or allosteric modulation, can be gained with experimental and computational studies. The latter play an important role in this process, since they allow for observations on scales inaccessible for most other methods. One of the key steps in such studies is proper computational reconstruction of actual ligand-receptor or protein-protein interactions, a process called molecular docking. A number of improvements and innovative applications of this method were documented recently. In this review, we focus particularly on innovations in docking to GPCRs.
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Affiliation(s)
- Damian Bartuzi
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modelling Lab, Medical University of Lublin, 4A Chodźki Str., PL20093 Lublin, Poland.
| | - Agnieszka A Kaczor
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modelling Lab, Medical University of Lublin, 4A Chodźki Str., PL20093 Lublin, Poland.
- School of Pharmacy, University of Eastern Finland, Yliopistonranta 1, P.O. Box 1627, FI-70211 Kuopio, Finland.
| | | | - Dariusz Matosiuk
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modelling Lab, Medical University of Lublin, 4A Chodźki Str., PL20093 Lublin, Poland.
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Fronik P, Gaiser BI, Sejer Pedersen D. Bitopic Ligands and Metastable Binding Sites: Opportunities for G Protein-Coupled Receptor (GPCR) Medicinal Chemistry. J Med Chem 2017; 60:4126-4134. [DOI: 10.1021/acs.jmedchem.6b01601] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Philipp Fronik
- Department of Drug Design
and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, 2100 Copenhagen, Denmark
| | - Birgit I. Gaiser
- Department of Drug Design
and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, 2100 Copenhagen, Denmark
| | - Daniel Sejer Pedersen
- Department of Drug Design
and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, 2100 Copenhagen, Denmark
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Kaczor AA, Jörg M, Capuano B. The dopamine D2 receptor dimer and its interaction with homobivalent antagonists: homology modeling, docking and molecular dynamics. J Mol Model 2016; 22:203. [PMID: 27491852 PMCID: PMC5023759 DOI: 10.1007/s00894-016-3065-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 07/03/2016] [Indexed: 01/11/2023]
Abstract
In order to apply structure-based drug design techniques to G protein-coupled receptor complexes, it is essential to model their 3D structure and to identify regions that are suitable for selective drug binding. For this purpose, we have developed and tested a multi-component protocol to model the inactive conformation of the dopamine D2 receptor dimer, suitable for interaction with homobivalent antagonists. Our approach was based on protein-protein docking, applying the Rosetta software to obtain populations of dimers as present in membranes with all the main possible interfaces. Consensus scoring based on the values and frequencies of best interfaces regarding four scoring parameters, Rosetta interface score, interface area, free energy of binding and energy of hydrogen bond interactions indicated that the best scored dimer model possesses a TM4-TM5-TM7-TM1 interface, which is in agreement with experimental data. This model was used to study interactions of the previously published dopamine D2 receptor homobivalent antagonists based on clozapine,1,4-disubstituted aromatic piperidines/piperazines and arylamidoalkyl substituted phenylpiperazine pharmacophores. It was found that the homobivalent antagonists stabilize the receptor-inactive conformation by maintaining the ionic lock interaction, and change the dimer interface by disrupting a set of hydrogen bonds and maintaining water- and ligand-mediated hydrogen bonds in the extracellular and intracellular part of the interface. Graphical Abstract Structure of the final model of the dopamine D2 receptor homodimer, indicating the distancebetween Tyr37 and Tyr 5.42 in the apo form (left) and in the complex with the ligand (right).
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Affiliation(s)
- Agnieszka A Kaczor
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modeling Laboratory, Faculty of Pharmacy with Division for Medical Analytics, Medical University of Lublin, 4A Chodźki St., 20059, Lublin, Poland.
- School of Pharmacy, University of Eastern Finland, Yliopistonranta 1, PO Box 1627, 70211, Kuopio, Finland.
| | - Manuela Jörg
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria, 3052, Australia
| | - Ben Capuano
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria, 3052, Australia
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18
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Multivalent approaches and beyond: novel tools for the investigation of dopamine D2 receptor pharmacology. Future Med Chem 2016; 8:1349-72. [DOI: 10.4155/fmc-2016-0010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The dopamine D2 receptor (D2R) has been implicated in the symptomology of disorders such as schizophrenia and Parkinson's disease. Multivalent ligands provide useful tools to investigate emerging concepts of G protein-coupled receptor drug action such as allostery, bitopic binding and receptor dimerization. This review focuses on the approaches taken toward the development of multivalent ligands for the D2R recently and highlights the challenges associated with each approach, their utility in probing D2R function and approaches to develop new D2R-targeting drugs. Furthermore, we extend our discussion to the possibility of designing multitarget ligands. The insights gained from such studies may provide the basis for improved therapeutic targeting of the D2R.
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Jörg M, Scammells PJ. Guidelines for the Synthesis of Small-Molecule Irreversible Probes Targeting G Protein-Coupled Receptors. ChemMedChem 2016; 11:1488-98. [PMID: 27347648 DOI: 10.1002/cmdc.201600066] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Revised: 06/07/2016] [Indexed: 02/03/2023]
Abstract
Irreversible probes have been proven to be useful pharmacological tools in the study of structural and functional features in drug receptor pharmacology. They have been demonstrated to be particularly valuable for the isolation and purification of receptors. Furthermore, irreversible probes are helpful tools for the identification and characterization of binding sites, thereby supporting the advancement of rational drug design. In this Minireview, we provide insight into universal strategies and guidelines to successfully synthesize irreversible probes that target G protein-coupled receptors (GPCRs). We provide an overview of commonly used chemoreactive and photoreactive groups, and make a comparison of their properties and potential applications. Furthermore, there is a particular focus on synthetic approaches to introduce these reactive groups based on commercially available reagents.
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Affiliation(s)
- Manuela Jörg
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, 3052, Victoria, Australia.
| | - Peter J Scammells
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, 3052, Victoria, Australia.
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Jörg M, May LT, Mak FS, Lee KCK, Miller ND, Scammells PJ, Capuano B. Synthesis and pharmacological evaluation of dual acting ligands targeting the adenosine A2A and dopamine D2 receptors for the potential treatment of Parkinson's disease. J Med Chem 2014; 58:718-38. [PMID: 25490054 DOI: 10.1021/jm501254d] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A relatively new strategy in drug discovery is the development of dual acting ligands. These molecules are potentially able to interact at two orthosteric binding sites of a heterodimer simultaneously, possibly resulting in enhanced subtype selectivity, higher affinity, enhanced or modified physiological response, and reduced reliance on multiple drug administration regimens. In this study, we have successfully synthesized a series of classical heterobivalent ligands as well as a series of more integrated and "drug-like" dual acting molecules, incorporating ropinirole as a dopamine D2 receptor agonist and ZM 241385 as an adenosine A2A receptor antagonist. The best compounds of our series maintained the potency of the original pharmacophores at both receptors (adenosine A2A and dopamine D2). In addition, the integrated dual acting ligands also showed promising results in preliminary blood-brain barrier permeability tests, whereas the classical heterobivalent ligands are potentially more suited as pharmacological tools.
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Affiliation(s)
- Manuela Jörg
- Medicinal Chemistry and ‡Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences , 381 Royal Parade, Parkville, Victoria 3052, Australia
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Jörg M, Headey S, Scammells PJ, Capuano B. NMR case study of ropinirole: concentration-dependent effects of nonexchangeable proton resonances. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2014; 52:715-718. [PMID: 25104507 DOI: 10.1002/mrc.4114] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Revised: 06/27/2014] [Accepted: 07/01/2014] [Indexed: 06/03/2023]
Affiliation(s)
- Manuela Jörg
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, 381 Royal Parade, Parkville, Victoria, 3052, Australia
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