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Distler K, Maschauer S, Neu E, Hübner H, Einsiedel J, Prante O, Gmeiner P. Structure-guided discovery of orexin receptor-binding PET ligands. Bioorg Med Chem 2024; 110:117823. [PMID: 38964170 DOI: 10.1016/j.bmc.2024.117823] [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: 05/03/2024] [Revised: 06/25/2024] [Accepted: 06/25/2024] [Indexed: 07/06/2024]
Abstract
Molecular imaging using positron emission tomography (PET) can serve as a promising tool for visualizing biological targets in the brain. Insights into the expression pattern and the in vivo imaging of the G protein-coupled orexin receptors OX1R and OX2R will further our understanding of the orexin system and its role in various physiological and pathophysiological processes. Guided by crystal structures of our lead compound JH112 and the approved hypnotic drug suvorexant bound to OX1R and OX2R, respectively, we herein describe the design and synthesis of two novel radioligands, [18F]KD23 and [18F]KD10. Key to the success of our structural modifications was a bioisosteric replacement of the triazole moiety with a fluorophenyl group. The 19F-substituted analog KD23 showed high affinity for the OX1R and selectivity over OX2R, while the high affinity ligand KD10 displayed similar Ki values for both subtypes. Radiolabeling starting from the respective pinacol ester precursors resulted in excellent radiochemical yields of 93% and 88% for [18F]KD23 and [18F]KD10, respectively, within 20 min. The new compounds will be useful in PET studies aimed at subtype-selective imaging of orexin receptors in brain tissue.
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Affiliation(s)
- Katharina Distler
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, 91058 Erlangen, Germany; FAU NeW - Research Center New Bioactive Compounds, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, 91058 Erlangen, Germany
| | - Simone Maschauer
- Department of Nuclear Medicine, Molecular Imaging and Radiochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Kussmaulallee 12, 91054 Erlangen, Germany
| | - Eduard Neu
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, 91058 Erlangen, Germany; FAU NeW - Research Center New Bioactive Compounds, 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; FAU NeW - Research Center New Bioactive Compounds, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, 91058 Erlangen, Germany
| | - Jürgen Einsiedel
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, 91058 Erlangen, Germany; FAU NeW - Research Center New Bioactive Compounds, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, 91058 Erlangen, Germany
| | - Olaf Prante
- FAU NeW - Research Center New Bioactive Compounds, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, 91058 Erlangen, Germany; Department of Nuclear Medicine, Molecular Imaging and Radiochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Kussmaulallee 12, 91054 Erlangen, Germany
| | - Peter Gmeiner
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, 91058 Erlangen, Germany; FAU NeW - Research Center New Bioactive Compounds, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, 91058 Erlangen, Germany.
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2
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Patient G, Bedart C, Khan NA, Renault N, Farce A. Distinct binding hotspots for natural and synthetic agonists of FFA4 from in silico approaches. Mol Inform 2024:e202400046. [PMID: 39046372 DOI: 10.1002/minf.202400046] [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: 02/05/2024] [Revised: 05/13/2024] [Accepted: 05/14/2024] [Indexed: 07/25/2024]
Abstract
FFA4 has gained interest in recent years since its deorphanization in 2005 and the characterization of the Free Fatty Acids receptors family for their therapeutic potential in metabolic disorders. The expression of FFA4 (also known as GPR120) in numerous organs throughout the human body makes this receptor a highly potent target, particularly in fat sensing and diet preference. This offers an attractive approach to tackle obesity and related metabolic diseases. Recent cryo-EM structures of the receptor have provided valuable information for a potential active state although the previous studies of FFA4 presented diverging information. We performed molecular docking and molecular dynamics simulations of four agonist ligands, TUG-891, Linoleic acid, α-Linolenic acid, and Oleic acid, based on a homology model. Our simulations, which accumulated a total of 2 μs of simulation, highlighted two binding hotspots at Arg992.64 and Lys293 (ECL3). The results indicate that the residues are located in separate areas of the binding pocket and interact with various types of ligands, implying different potential active states of FFA4 and a highly adaptable binding intra-receptor pocket. This article proposes additional structural characteristics and mechanisms for agonist binding that complement the experimental structures.
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Affiliation(s)
- Guillaume Patient
- University of Lille, Inserm, CHU Lille, U1286 - INFINITE-Institute for Translational Research in Inflammation, F-59000, Lille, France
| | - Corentin Bedart
- University of Lille, Inserm, CHU Lille, U1286 - INFINITE-Institute for Translational Research in Inflammation, F-59000, Lille, France
| | - Naim A Khan
- U1231 Inserm, Equipe NuTox, AgroSup, Université de Bourgogne, Dijon, France
| | - Nicolas Renault
- University of Lille, Inserm, CHU Lille, U1286 - INFINITE-Institute for Translational Research in Inflammation, F-59000, Lille, France
| | - Amaury Farce
- University of Lille, Inserm, CHU Lille, U1286 - INFINITE-Institute for Translational Research in Inflammation, F-59000, Lille, France
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3
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Szwabowski GL, Griffing M, Mugabe EJ, O'Malley D, Baker LN, Baker DL, Parrill AL. G Protein-Coupled Receptor-Ligand Pose and Functional Class Prediction. Int J Mol Sci 2024; 25:6876. [PMID: 38999982 PMCID: PMC11241240 DOI: 10.3390/ijms25136876] [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: 05/24/2024] [Revised: 06/13/2024] [Accepted: 06/19/2024] [Indexed: 07/14/2024] Open
Abstract
G protein-coupled receptor (GPCR) transmembrane protein family members play essential roles in physiology. Numerous pharmaceuticals target GPCRs, and many drug discovery programs utilize virtual screening (VS) against GPCR targets. Improvements in the accuracy of predicting new molecules that bind to and either activate or inhibit GPCR function would accelerate such drug discovery programs. This work addresses two significant research questions. First, do ligand interaction fingerprints provide a substantial advantage over automated methods of binding site selection for classical docking? Second, can the functional status of prospective screening candidates be predicted from ligand interaction fingerprints using a random forest classifier? Ligand interaction fingerprints were found to offer modest advantages in sampling accurate poses, but no substantial advantage in the final set of top-ranked poses after scoring, and, thus, were not used in the generation of the ligand-receptor complexes used to train and test the random forest classifier. A binary classifier which treated agonists, antagonists, and inverse agonists as active and all other ligands as inactive proved highly effective in ligand function prediction in an external test set of GPR31 and TAAR2 candidate ligands with a hit rate of 82.6% actual actives within the set of predicted actives.
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Affiliation(s)
| | - Makenzie Griffing
- Department of Chemistry, University of Memphis, Memphis, TN 38152, USA
| | - Elijah J Mugabe
- Department of Chemistry, University of Memphis, Memphis, TN 38152, USA
| | - Daniel O'Malley
- Department of Chemistry, University of Memphis, Memphis, TN 38152, USA
| | - Lindsey N Baker
- Department of Chemistry, University of Memphis, Memphis, TN 38152, USA
| | - Daniel L Baker
- Department of Chemistry, University of Memphis, Memphis, TN 38152, USA
| | - Abby L Parrill
- Department of Chemistry, University of Memphis, Memphis, TN 38152, USA
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4
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Zhang VY, O'Connor SL, Welsh WJ, James MH. Machine learning models to predict ligand binding affinity for the orexin 1 receptor. ARTIFICIAL INTELLIGENCE CHEMISTRY 2024; 2:100040. [PMID: 38476266 PMCID: PMC10927255 DOI: 10.1016/j.aichem.2023.100040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/14/2024]
Abstract
The orexin 1 receptor (OX1R) is a G-protein coupled receptor that regulates a variety of physiological processes through interactions with the neuropeptides orexin A and B. Selective OX1R antagonists exhibit therapeutic effects in preclinical models of several behavioral disorders, including drug seeking and overeating. However, currently there are no selective OX1R antagonists approved for clinical use, fueling demand for novel compounds that act at this target. In this study, we meticulously curated a dataset comprising over 1300 OX1R ligands using a stringent filter and criteria cascade. Subsequently, we developed highly predictive quantitative structure-activity relationship (QSAR) models employing the optimized hyper-parameters for the random forest machine learning algorithm and twelve 2D molecular descriptors selected by recursive feature elimination with a 5-fold cross-validation process. The predictive capacity of the QSAR model was further assessed using an external test set and enrichment study, confirming its high predictivity. The practical applicability of our final QSAR model was demonstrated through virtual screening of the DrugBank database. This revealed two FDA-approved drugs (isavuconazole and cabozantinib) as potential OX1R ligands, confirmed by radiolabeled OX1R binding assays. To our best knowledge, this study represents the first report of highly predictive QSAR models on a large comprehensive dataset of diverse OX1R ligands, which should prove useful for the discovery and design of new compounds targeting this receptor.
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Affiliation(s)
- Vanessa Y Zhang
- Department of Psychiatry, Robert Wood Johnson Medical School, Rutgers University and Rutgers Biomedical Health Sciences, Piscataway, NJ, USA
- Brain Health Institute, Rutgers University and Rutgers Biomedical and Health Sciences, Piscataway, NJ, USA
- West Windsor-Plainsboro High School South, West Windsor, NJ, USA
| | - Shayna L O'Connor
- Department of Psychiatry, Robert Wood Johnson Medical School, Rutgers University and Rutgers Biomedical Health Sciences, Piscataway, NJ, USA
- Brain Health Institute, Rutgers University and Rutgers Biomedical and Health Sciences, Piscataway, NJ, USA
| | - William J Welsh
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers University and Rutgers Biomedical Health Sciences, Piscataway, NJ, USA
| | - Morgan H James
- Department of Psychiatry, Robert Wood Johnson Medical School, Rutgers University and Rutgers Biomedical Health Sciences, Piscataway, NJ, USA
- Brain Health Institute, Rutgers University and Rutgers Biomedical and Health Sciences, Piscataway, NJ, USA
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5
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Imamura K, Akagi KI, Miyanoiri Y, Tsujimoto H, Hirokawa T, Ashida H, Murakami K, Inoue A, Suno R, Ikegami T, Sekiyama N, Iwata S, Kobayashi T, Tochio H. Interaction modes of human orexin 2 receptor with selective and nonselective antagonists studied by NMR spectroscopy. Structure 2024; 32:352-361.e5. [PMID: 38194963 DOI: 10.1016/j.str.2023.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 08/17/2023] [Accepted: 12/13/2023] [Indexed: 01/11/2024]
Abstract
Orexin neuropeptides have many physiological roles in the sleep-wake cycle, feeding behavior, reward demands, and stress responses by activating cognitive receptors, the orexin receptors (OX1R and OX2R), distributed in the brain. There are only subtle differences between OX1R and OX2R in the orthosteric site, which has hindered the rational development of subtype-selective antagonists. In this study, we utilized solution-state NMR to capture the structural plasticity of OX2R labeled with 13CH3-ε-methionine in complex with antagonists. Mutations in the orthosteric site allosterically affected the intracellular tip of TM6. Ligand exchange experiments with the subtype-selective EMPA and the nonselective suvorexant identified three methionine residues that were substantially perturbed. The NMR spectra suggested that the suvorexant-bound state exhibited more structural plasticity than the EMPA-bound state, which has not been foreseen from the close similarity of their crystal structures, providing insights into dynamic features to be considered in understanding the ligand recognition mode.
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Affiliation(s)
- Kayo Imamura
- Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Ken-Ichi Akagi
- Section of Laboratory Equipment, National Institute of Biomedical Innovation, Health, and Nutrition, Osaka 567-0085, Japan
| | - Yohei Miyanoiri
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Hirokazu Tsujimoto
- Department of Cell Biology and Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Takatsugu Hirokawa
- Division of Biomedical Science, Faculty of Medicine, University of Tsukuba, Tsukuba 305-8575, Japan; Transborder Medical Research Center, University of Tsukuba, Tsukuba 305-8575, Japan
| | - Hideo Ashida
- Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Kaori Murakami
- Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Asuka Inoue
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan
| | - Ryoji Suno
- Department of Medical Chemistry, Kansai Medical University, Hirakata 573-1010, Japan
| | - Takahisa Ikegami
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro, Yokohama, Kanagawa 230-0045, Japan
| | - Naotaka Sekiyama
- Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - So Iwata
- Department of Cell Biology and Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Takuya Kobayashi
- Department of Medical Chemistry, Kansai Medical University, Hirakata 573-1010, Japan
| | - Hidehito Tochio
- Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan.
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6
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Glen A, Bürli RW, Livermore D, Buffham W, Merison S, Rowland AE, Newman R, Fieldhouse C, Miller DJ, Dawson LA, Matthews K, Carlton MB, Brice NL. Discovery and first-time disclosure of CVN766, an exquisitely selective orexin 1 receptor antagonist. Bioorg Med Chem Lett 2024; 100:129629. [PMID: 38295907 DOI: 10.1016/j.bmcl.2024.129629] [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: 09/08/2023] [Revised: 01/15/2024] [Accepted: 01/26/2024] [Indexed: 02/10/2024]
Abstract
Modulators of orexin receptors are being developed for neurological illnesses such as sleep disorders, addictive behaviours and other psychiatric diseases. We herein describe the discovery of CVN766, a potent orexin 1 receptor antagonist that has greater than 1000-fold selectivity for the orexin 1 receptor over the orexin 2 receptor and demonstrates low off target hits in a diversity screen. In agreement with its in vitro ADME data, CVN766 demonstrated moderate in vivo clearance in rodents and displayed good brain permeability and target occupancy. This drug candidate is currently being investigated in clinical trials for schizophrenia and related psychiatric conditions.
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Affiliation(s)
- Angela Glen
- Takeda Cambridge Ltd., 418 Cambridge Science Park, Milton Road, Cambridge CB4 0PZ, UK
| | - Roland W Bürli
- Cerevance Ltd, 418 Cambridge Science Park, Milton Road, Cambridge CB4 0PZ, UK
| | - David Livermore
- Takeda Cambridge Ltd., 418 Cambridge Science Park, Milton Road, Cambridge CB4 0PZ, UK
| | - William Buffham
- Takeda Cambridge Ltd., 418 Cambridge Science Park, Milton Road, Cambridge CB4 0PZ, UK
| | - Stephanie Merison
- Takeda Cambridge Ltd., 418 Cambridge Science Park, Milton Road, Cambridge CB4 0PZ, UK
| | - Anna E Rowland
- Takeda Cambridge Ltd., 418 Cambridge Science Park, Milton Road, Cambridge CB4 0PZ, UK; Cerevance Ltd, 418 Cambridge Science Park, Milton Road, Cambridge CB4 0PZ, UK
| | - Robert Newman
- Takeda Cambridge Ltd., 418 Cambridge Science Park, Milton Road, Cambridge CB4 0PZ, UK; Cerevance Ltd, 418 Cambridge Science Park, Milton Road, Cambridge CB4 0PZ, UK
| | - Charlotte Fieldhouse
- Takeda Cambridge Ltd., 418 Cambridge Science Park, Milton Road, Cambridge CB4 0PZ, UK
| | - David J Miller
- Takeda Cambridge Ltd., 418 Cambridge Science Park, Milton Road, Cambridge CB4 0PZ, UK
| | - Lee A Dawson
- Cerevance Ltd, 418 Cambridge Science Park, Milton Road, Cambridge CB4 0PZ, UK
| | - Kim Matthews
- Cerevance Ltd, 418 Cambridge Science Park, Milton Road, Cambridge CB4 0PZ, UK
| | - Mark B Carlton
- Takeda Cambridge Ltd., 418 Cambridge Science Park, Milton Road, Cambridge CB4 0PZ, UK; Cerevance Ltd, 418 Cambridge Science Park, Milton Road, Cambridge CB4 0PZ, UK
| | - Nicola L Brice
- Takeda Cambridge Ltd., 418 Cambridge Science Park, Milton Road, Cambridge CB4 0PZ, UK; Cerevance Ltd, 418 Cambridge Science Park, Milton Road, Cambridge CB4 0PZ, UK.
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7
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Yuan S, Shen DD, Jia R, Sun JS, Song J, Liu HM. New drug approvals for 2022: Synthesis and clinical applications. Med Res Rev 2023; 43:2352-2391. [PMID: 37211904 DOI: 10.1002/med.21976] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 04/13/2023] [Accepted: 05/08/2023] [Indexed: 05/23/2023]
Abstract
The U.S. Food and Drug Administration has approved a total of 37 new drugs in 2022, which are composed of 20 chemical entities and 17 biologics. In particular, 20 chemical entities, including 17 small molecule drugs, 1 radiotherapy, and 2 diagnostic agents, provide privileged scaffolds, breakthrough clinical benefits, and a new mechanism of action for the discovery of more potent clinical candidates. The structure-based drug development with clear targets and fragment-based drug development with privileged scaffolds have always been the important modules in the field of drug discovery, which could easily bypass the patent protection and bring about improved biological activity. Therefore, we summarized the relevant valuable information about clinical application, mechanism of action, and chemical synthesis of 17 newly approved small molecule drugs in 2022. We hope this timely and comprehensive review could bring about creative and elegant inspiration on the synthetic methodologies and mechanism of action for the discovery of new drugs with novel chemical scaffolds and extended clinical indications.
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Affiliation(s)
- Shuo Yuan
- Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, China
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Zhengzhou University, Zhengzhou, China
- Department of Pharmacology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Dan-Dan Shen
- Department of Obstetrics and Gynecology, Zhengzhou Key Laboratory of Endometrial Disease Prevention and Treatment Zhengzhou China, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Rui Jia
- Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, China
| | - Ju-Shan Sun
- Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, China
| | - Jian Song
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Zhengzhou University, Zhengzhou, China
- Department of Pharmacology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Hong-Min Liu
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Zhengzhou University, Zhengzhou, China
- Department of Pharmacology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
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Bonifazi A, Del Bello F, Giorgioni G, Piergentili A, Saab E, Botticelli L, Cifani C, Micioni Di Bonaventura E, Micioni Di Bonaventura MV, Quaglia W. Targeting orexin receptors: Recent advances in the development of subtype selective or dual ligands for the treatment of neuropsychiatric disorders. Med Res Rev 2023; 43:1607-1667. [PMID: 37036052 DOI: 10.1002/med.21959] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 03/08/2023] [Accepted: 03/28/2023] [Indexed: 04/11/2023]
Abstract
Orexin-A and orexin-B, also named hypocretin-1 and hypocretin-2, are two hypothalamic neuropeptides highly conserved across mammalian species. Their effects are mediated by two distinct G protein-coupled receptors, namely orexin receptor type 1 (OX1-R) and type 2 (OX2-R), which share 64% amino acid identity. Given the wide expression of OX-Rs in different central nervous system and peripheral areas and the several pathophysiological functions in which they are involved, including sleep-wake cycle regulation (mainly mediated by OX2-R), emotion, panic-like behaviors, anxiety/stress, food intake, and energy homeostasis (mainly mediated by OX1-R), both subtypes represent targets of interest for many structure-activity relationship (SAR) campaigns carried out by pharmaceutical companies and academies. However, before 2017 the research was predominantly directed towards dual-orexin ligands, and limited chemotypes were investigated. Analytical characterizations, including resolved structures for both OX1-R and OX2-R in complex with agonists and antagonists, have improved the understanding of the molecular basis of receptor recognition and are assets for medicinal chemists in the design of subtype-selective ligands. This review is focused on the medicinal chemistry aspects of small molecules acting as dual or subtype selective OX1-R/OX2-R agonists and antagonists belonging to different chemotypes and developed in the last years, including radiolabeled OX-R ligands for molecular imaging. Moreover, the pharmacological effects of the most studied ligands in different neuropsychiatric diseases, such as sleep, mood, substance use, and eating disorders, as well as pain, have been discussed. Poly-pharmacology applications and multitarget ligands have also been considered.
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Affiliation(s)
- Alessandro Bonifazi
- Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse - Intramural Research Program, National Institutes of Health, Baltimore, Maryland, United States
| | - Fabio Del Bello
- School of Pharmacy, Medicinal Chemistry Unit, University of Camerino, Camerino, Italy
| | - Gianfabio Giorgioni
- School of Pharmacy, Medicinal Chemistry Unit, University of Camerino, Camerino, Italy
| | | | - Elizabeth Saab
- Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse - Intramural Research Program, National Institutes of Health, Baltimore, Maryland, United States
| | - Luca Botticelli
- School of Pharmacy, Pharmacology Unit, University of Camerino, Camerino, Italy
| | - Carlo Cifani
- School of Pharmacy, Pharmacology Unit, University of Camerino, Camerino, Italy
| | | | | | - Wilma Quaglia
- School of Pharmacy, Medicinal Chemistry Unit, University of Camerino, Camerino, Italy
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9
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Zhao H, Brånalt J, Perry M, Tyrchan C. The Role of Allylic Strain for Conformational Control in Medicinal Chemistry. J Med Chem 2023. [PMID: 37285219 DOI: 10.1021/acs.jmedchem.3c00446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
It is axiomatic in medicinal chemistry that optimization of the potency of a small molecule at a macromolecular target requires complementarity between the ligand and target. In order to minimize the conformational penalty on binding, both enthalpically and entropically, it is therefore preferred to have the ligand preorganized in the bound conformation. In this Perspective, we highlight the role of allylic strain in controlling conformational preferences. Allylic strain was originally described for carbon-based allylic systems, but the same principles apply to other types of structure with sp2 or pseudo-sp2 arrangements. These systems include benzylic (including heteroaryl methyl) positions, amides, N-aryl groups, aryl ethers, and nucleotides. We have derived torsion profiles from small molecule X-ray structures for these systems. Through multiple examples, we show how these effects have been applied in drug discovery and how they can be used prospectively to influence conformation in the design process.
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Affiliation(s)
- Hongtao Zhao
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology (R&I), BioPharmaceuticals R&D, AstraZeneca, Gothenburg 43183, Sweden
| | - Jonas Brånalt
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg 43183, Sweden
| | - Matthew Perry
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology (R&I), BioPharmaceuticals R&D, AstraZeneca, Gothenburg 43183, Sweden
| | - Christian Tyrchan
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology (R&I), BioPharmaceuticals R&D, AstraZeneca, Gothenburg 43183, Sweden
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10
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Moline M, Asakura S, Beuckman C, Landry I, Setnik B, Ashworth J, Henningfield JE. The abuse potential of lemborexant, a dual orexin receptor antagonist, according to the 8 factors of the Controlled Substances Act. Psychopharmacology (Berl) 2023; 240:699-711. [PMID: 36749354 PMCID: PMC10006052 DOI: 10.1007/s00213-023-06320-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 01/17/2023] [Indexed: 02/08/2023]
Abstract
RATIONALE Lemborexant (LEM) is a dual orexin receptor antagonist (DORA) approved in multiple countries including the USA, Japan, Canada, Australia, and several Asian countries for the treatment of insomnia in adults. As a compound with central nervous system activity, it is important to understand the abuse potential of LEM with respect to public health. OBJECTIVES This review discusses data for LEM relevant to each of the 8 factors of the United States Controlled Substances Act. RESULTS LEM did not demonstrate abuse potential in nonclinical testing and was associated with a low incidence of abuse-related adverse events in clinical study participants with insomnia disorder. Similar to other DORAs that have been evaluated (eg., almorexant, suvorexant (SUV), and daridorexant), LEM and the positive controls (zolpidem and SUV) also showed drug liking in a phase 1 abuse potential study that enrolled subjects who used sedatives recreationally. However, internet surveillance of SUV and the FDA Adverse Events Reporting System suggests that drugs in the DORA class display very low abuse-related risks in the community. Additionally, as described in FDA-approved labeling, it does not carry physical dependence and withdrawal risks. CONCLUSIONS LEM, similar to most other prescription insomnia medications, was placed into Schedule IV. However, LEM and other drugs in the DORA class may have a lower potential for abuse as suggested by real-world postmarketing data from federal surveys and internet surveillance, and thus may have lower risks to public health than Schedule IV benzodiazepines and nonbenzodiazepine hypnotics that potentiate GABA signaling.
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Affiliation(s)
- Margaret Moline
- Eisai Inc., 200 Metro Boulevard, Nutley, Jersey, NJ, 07110, USA.
| | | | | | | | - Beatrice Setnik
- Altasciences, Laval, Quebec, Canada and the Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada
| | | | - Jack E Henningfield
- Pinney Associates, Inc., Bethesda, MD, USA.,The Johns Hopkins University School of Medicine, Baltimore, MD, USA
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11
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Amezawa M, Yamamoto N, Nagumo Y, Kutsumura N, Ishikawa Y, Yanagisawa M, Nagase H, Saitoh T. Design and synthesis of novel orexin 2 receptor agonists with a 1,3,5‑trioxazatriquinane skeleton. Bioorg Med Chem Lett 2023; 82:129151. [PMID: 36690040 DOI: 10.1016/j.bmcl.2023.129151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 01/16/2023] [Accepted: 01/18/2023] [Indexed: 01/21/2023]
Abstract
A novel series of 1,3,5‑trioxazatriquinane with multiple effective residues (TriMER) derivatives with amino-methylene side chains was designed and synthesized based on the docking-simulation results between orexin receptors (OXRs) and TriMER-type OXR antagonists. In vitro screening against orexin receptors identified six TriMER derivatives with a cis side-chain configuration, and, among these, 20d and 28d showed full agonist activity against OX2R at a concentration of 10 µM. To determine the absolute stereochemistry of these hit compounds, we also conducted the first asymmetric synthesis of a 1,3,5‑trioxazatriquinane skeleton using a Katsuki-Sharpless asymmetric epoxidation as the key reaction and obtained a set of the individual stereoisomers. After evaluating their activity, (+)-20d (EC50 = 3.87 μM for OX2R) and (+)-28d (EC50 = 1.62 μM for OX2R) were determined as eutomers for OX2R agonist activity. Our results provide a new class of skeleton consisting of an (R)-1,3,5‑trioxazatriquinane core with flexible methylene linkers and hydrophobic substituents at the terminals of the side chains via carbamates/sulfonamides as OX2R agonists.
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Affiliation(s)
- Mao Amezawa
- Graduate School of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8571, Japan
| | - Naoshi Yamamoto
- International Institute for Integrative Sleep Medicine (IIIS), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Yasuyuki Nagumo
- International Institute for Integrative Sleep Medicine (IIIS), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Noriki Kutsumura
- Graduate School of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8571, Japan; International Institute for Integrative Sleep Medicine (IIIS), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan; Graduate School of Comprehensive Human Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Yukiko Ishikawa
- International Institute for Integrative Sleep Medicine (IIIS), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Masashi Yanagisawa
- International Institute for Integrative Sleep Medicine (IIIS), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan; R&D Center for Frontiers of Mirai in Policy and Technology (F-MIRAI), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan; Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX 75390, US
| | - Hiroshi Nagase
- Graduate School of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8571, Japan; International Institute for Integrative Sleep Medicine (IIIS), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan.
| | - Tsuyoshi Saitoh
- International Institute for Integrative Sleep Medicine (IIIS), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan; Graduate School of Comprehensive Human Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan.
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12
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Dmitrieva DA, Kotova TV, Safronova NA, Sadova AA, Dashevskii DE, Mishin AV. Protein Design Strategies for the Structural–Functional Studies of G Protein-Coupled Receptors. BIOCHEMISTRY (MOSCOW) 2023; 88:S192-S226. [PMID: 37069121 DOI: 10.1134/s0006297923140110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
G protein-coupled receptors (GPCRs) are an important family of membrane proteins responsible for many physiological functions in human body. High resolution GPCR structures are required to understand their molecular mechanisms and perform rational drug design, as GPCRs play a crucial role in a variety of diseases. That is difficult to obtain for the wild-type proteins because of their low stability. In this review, we discuss how this problem can be solved by using protein design strategies developed to obtain homogeneous stabilized GPCR samples for crystallization and cryoelectron microscopy.
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Affiliation(s)
- Daria A Dmitrieva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Tatiana V Kotova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Nadezda A Safronova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Alexandra A Sadova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Dmitrii E Dashevskii
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Alexey V Mishin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia.
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13
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Molecular basis for anti-insomnia drug design from structure of lemborexant-bound orexin 2 receptor. Structure 2022; 30:1582-1589.e4. [DOI: 10.1016/j.str.2022.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 09/24/2022] [Accepted: 10/28/2022] [Indexed: 11/23/2022]
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14
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Raïch I, Rebassa JB, Lillo J, Cordomi A, Rivas-Santisteban R, Lillo A, Reyes-Resina I, Franco R, Navarro G. Antagonization of OX 1 Receptor Potentiates CB 2 Receptor Function in Microglia from APP Sw/Ind Mice Model. Int J Mol Sci 2022; 23:12801. [PMID: 36361598 PMCID: PMC9656664 DOI: 10.3390/ijms232112801] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 10/04/2022] [Accepted: 10/14/2022] [Indexed: 08/01/2023] Open
Abstract
Microdialysis assays demonstrated a possible role of orexin in the regulation of amyloid beta peptide (Aß) levels in the hippocampal interstitial fluid in the APP transgenic model. CB2R is overexpressed in activated microglia, showing a neuroprotective effect. These two receptors may interact, forming CB2-OX1-Hets and becoming a new target to combat Alzheimer's disease. Aims: Demonstrate the potential role of CB2-OX1-Hets expression and function in microglia from animal models of Alzheimer's disease. Receptor heteromer expression was detected by immunocytochemistry, bioluminescence resonance energy transfer (BRET) and proximity ligation assay (PLA) in transfected HEK-293T cells and microglia primary cultures. Quantitation of signal transduction events in a heterologous system and in microglia cells was performed using the AlphaScreen® SureFire® kit, western blot, the GCaMP6 calcium sensor and the Lance Ultra cAMP kit (PerkinElmer). The formation of CB2-OX1 receptor complexes in transfected HEK-293T cells has been demonstrated. The tetrameric complex is constituted by one CB2R homodimer, one OX1R homodimer and two G proteins, a Gi and a Gq. The use of TAT interfering peptides showed that the CB2-OX1 receptor complex interface is TM4-TM5. At the functional level it has been observed that the OX1R antagonist, SB334867, potentiates the action induced by CB2R agonist JWH133. This effect is observed in transfected HEK-293T cells and microglia, and it is stronger in the Alzheimer's disease (AD) animal model APPSw/Ind where the expression of the complex assessed by the proximity ligation assay indicates an increase in the number of complexes compared to resting microglia. The CB2-OX1 receptor complex is overexpressed in microglia from AD animal models where OX1R antagonists potentiate the neuroprotective actions of CB2R activation. Taken together, these results point to OX1R antagonists as drugs with therapeutic potential to combat AD. Data access statement: Raw data will be provided by the corresponding author upon reasonable requirement.
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Affiliation(s)
- Iu Raïch
- Molecular Neuropharmacology Laboratory, Department of Biochemistry and Physiology, School of Pharmacy and Food Science, Universitat de Barcelona, 08007 Barcelona, Spain
- CiberNed, Network Center for Neurodegenerative Diseases, National Spanish Health Institute Carlos III, 28029 Madrid, Spain
- Neurosciences Institut, University of Barcelona (NeuroUB), 08028 Barcelona, Spain
| | - Joan Biel Rebassa
- Molecular Neuropharmacology Laboratory, Department of Biochemistry and Physiology, School of Pharmacy and Food Science, Universitat de Barcelona, 08007 Barcelona, Spain
- CiberNed, Network Center for Neurodegenerative Diseases, National Spanish Health Institute Carlos III, 28029 Madrid, Spain
- Neurosciences Institut, University of Barcelona (NeuroUB), 08028 Barcelona, Spain
| | - Jaume Lillo
- CiberNed, Network Center for Neurodegenerative Diseases, National Spanish Health Institute Carlos III, 28029 Madrid, Spain
- Neurosciences Institut, University of Barcelona (NeuroUB), 08028 Barcelona, Spain
| | | | - Rafael Rivas-Santisteban
- CiberNed, Network Center for Neurodegenerative Diseases, National Spanish Health Institute Carlos III, 28029 Madrid, Spain
- Neurosciences Institut, University of Barcelona (NeuroUB), 08028 Barcelona, Spain
| | - Alejandro Lillo
- Molecular Neuropharmacology Laboratory, Department of Biochemistry and Physiology, School of Pharmacy and Food Science, Universitat de Barcelona, 08007 Barcelona, Spain
- CiberNed, Network Center for Neurodegenerative Diseases, National Spanish Health Institute Carlos III, 28029 Madrid, Spain
- Neurosciences Institut, University of Barcelona (NeuroUB), 08028 Barcelona, Spain
| | - Irene Reyes-Resina
- Molecular Neuropharmacology Laboratory, Department of Biochemistry and Physiology, School of Pharmacy and Food Science, Universitat de Barcelona, 08007 Barcelona, Spain
- CiberNed, Network Center for Neurodegenerative Diseases, National Spanish Health Institute Carlos III, 28029 Madrid, Spain
- Neurosciences Institut, University of Barcelona (NeuroUB), 08028 Barcelona, Spain
| | - Rafael Franco
- Molecular Neuropharmacology Laboratory, Department of Biochemistry and Physiology, School of Pharmacy and Food Science, Universitat de Barcelona, 08007 Barcelona, Spain
- School of Chemistry, Universitat de Barcelona, 08007 Barcelona, Spain
| | - Gemma Navarro
- Molecular Neuropharmacology Laboratory, Department of Biochemistry and Physiology, School of Pharmacy and Food Science, Universitat de Barcelona, 08007 Barcelona, Spain
- CiberNed, Network Center for Neurodegenerative Diseases, National Spanish Health Institute Carlos III, 28029 Madrid, Spain
- Neurosciences Institut, University of Barcelona (NeuroUB), 08028 Barcelona, Spain
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15
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Thomas M, O'Boyle NM, Bender A, de Graaf C. Augmented Hill-Climb increases reinforcement learning efficiency for language-based de novo molecule generation. J Cheminform 2022; 14:68. [PMID: 36192789 PMCID: PMC9531503 DOI: 10.1186/s13321-022-00646-z] [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] [Received: 04/14/2022] [Accepted: 09/23/2022] [Indexed: 11/10/2022] Open
Abstract
A plethora of AI-based techniques now exists to conduct de novo molecule generation that can devise molecules conditioned towards a particular endpoint in the context of drug design. One popular approach is using reinforcement learning to update a recurrent neural network or language-based de novo molecule generator. However, reinforcement learning can be inefficient, sometimes requiring up to 105 molecules to be sampled to optimize more complex objectives, which poses a limitation when using computationally expensive scoring functions like docking or computer-aided synthesis planning models. In this work, we propose a reinforcement learning strategy called Augmented Hill-Climb based on a simple, hypothesis-driven hybrid between REINVENT and Hill-Climb that improves sample-efficiency by addressing the limitations of both currently used strategies. We compare its ability to optimize several docking tasks with REINVENT and benchmark this strategy against other commonly used reinforcement learning strategies including REINFORCE, REINVENT (version 1 and 2), Hill-Climb and best agent reminder. We find that optimization ability is improved ~ 1.5-fold and sample-efficiency is improved ~ 45-fold compared to REINVENT while still delivering appealing chemistry as output. Diversity filters were used, and their parameters were tuned to overcome observed failure modes that take advantage of certain diversity filter configurations. We find that Augmented Hill-Climb outperforms the other reinforcement learning strategies used on six tasks, especially in the early stages of training or for more difficult objectives. Lastly, we show improved performance not only on recurrent neural networks but also on a reinforcement learning stabilized transformer architecture. Overall, we show that Augmented Hill-Climb improves sample-efficiency for language-based de novo molecule generation conditioning via reinforcement learning, compared to the current state-of-the-art. This makes more computationally expensive scoring functions, such as docking, more accessible on a relevant timescale.
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Affiliation(s)
- Morgan Thomas
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK.
| | - Noel M O'Boyle
- Computational Chemistry, Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge, CB21 6DG, UK
| | - Andreas Bender
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Chris de Graaf
- Computational Chemistry, Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge, CB21 6DG, UK
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16
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Farrokhpour H, Bamdad F, Ashrafizaadeh M. Interaction between the Human OX2 Orexin Receptor and Suvorexant and Some of Its Analogues: SAPT (DFT) Interaction Energy Decomposition Analysis. J Phys Chem B 2022; 126:7528-7540. [PMID: 36166366 DOI: 10.1021/acs.jpcb.2c02537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this study, the interaction energy (Eint) of suvorexant (as an orexin receptor antagonist) and some of its analogues with the important residues of the human OX2 orexin receptor, determined by molecular docking, is calculated using the symmetry-adapted perturbation theory-density functional theory (SAPT (DFT)) method. Also, the important residues with the dominant interaction with each ligand are determined based on the obtained SAPT (DFT) interaction energies. To analyze the interaction of the receptor with each ligand, the decomposition of Eint to its constituent components including electrostatic (Eele), exchange (Eex), induction (Eind), and exchange-induction (Eex-ind), dispersion (Edisp), and exchange-dispersion (Eex-disp) is performed. The change of interaction energy components with the replacement of the benzoxazole part of suvorexant by pyrimidine containing different functional groups, thieno pyrimidine, and furo pyrimidine is also investigated, separately. It is found that the change in Eint, due to these replacements, is controlled more by the variation of the electrostatic interaction energy component of Eint than by the other interaction energy components. A linear correlation (R2 = 0.91) is found for the variation of Eint versus experimental ligand-binding affinities. Also, the existence of the linear correlation for the variation of the interaction energy components with experimental ligand-binding affinities is investigated. The variation of the electrostatic component versus experimental ligand-binding affinities shows a more linear correlation compared to the other interaction energy components.
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Affiliation(s)
- Hossein Farrokhpour
- Department of Chemistry, Isfahan University of Technology, Isfahan 84156-83111, Iran
| | - Fatemeh Bamdad
- Department of Chemistry, Isfahan University of Technology, Isfahan 84156-83111, Iran
| | - Mahmud Ashrafizaadeh
- Department of Mechanical Engineering, Isfahan University of Technology, Isfahan 84156-83111, Iran
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17
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Meanwell NA, Loiseleur O. Applications of Isosteres of Piperazine in the Design of Biologically Active Compounds: Part 2. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:10972-11004. [PMID: 35675052 DOI: 10.1021/acs.jafc.2c00729] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Applications of piperazine and homopiperazine in drug design are well-established, and these heterocycles have found use as both scaffolding and terminal elements and also as a means of introducing a water-solubilizing element into a molecule. In the accompanying review (10.1021/acs.jafc.2c00726), we summarized applications of piperazine and homopiperazine and their fused ring homologues in bioactive compound design along with illustrations of the use of 4-substituted piperidines and a sulfoximine-based mimetic. In this review, we discuss applications of pyrrolidine- and fused-pyrrolidine-based mimetics of piperazine and homopiperazine and illustrate derivatives of azetidine that include stretched and spirocyclic motifs, along with applications of a series of diaminocycloalkanes.
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Affiliation(s)
- Nicholas A Meanwell
- Small Molecule Drug Discovery, Bristol Myers Squibb Research and Early Development, Post Office Box 4000, Princeton, New Jersey 08543, United States
| | - Olivier Loiseleur
- Syngenta Crop Protection Research, Schaffhauserstrasse, CH-4332 Stein, Switzerland
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18
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Meanwell NA, Loiseleur O. Applications of Isosteres of Piperazine in the Design of Biologically Active Compounds: Part 1. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:10942-10971. [PMID: 35675050 DOI: 10.1021/acs.jafc.2c00726] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Piperazine and homopiperazine are well-studied heterocycles in drug design that have found gainful application as scaffolds and terminal elements and for enhancing the aqueous solubility of a molecule. The optimization of drug candidates that incorporate these heterocycles in an effort to refine potency, selectivity, and developability properties has stimulated the design and evaluation of a wide range of bioisosteres that can offer advantage. In this review, we summarize the design and application of bioisosteres of piperazine and homopiperazine that have almost exclusively been in the drug design arena. While there are ∼100 approved drugs that incorporate a piperazine ring, only a single marketed agricultural product is built on this heterocycle. As part of the review, we discuss some of the potential reasons underlying the relatively low level of importance of this heterocycle to the design of agrochemicals and highlight the potential opportunities for their use in contemporary research programs.
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Affiliation(s)
- Nicholas A Meanwell
- Small Molecule Drug Discovery, Bristol Myers Squibb Research and Early Development, PO Box 4000, Princeton, New Jersey 08543, United States
| | - Olivier Loiseleur
- Syngenta Crop Protection Research, Schaffhauserstrasse, Stein CH-4332, Switzerland
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19
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Dos Santos JBR, da Silva MRR. Daridorexant for the treatment of insomnia disorder: findings and implications. Eur J Clin Pharmacol 2022; 78:1749-1761. [PMID: 36098753 DOI: 10.1007/s00228-022-03381-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 09/03/2022] [Indexed: 11/03/2022]
Abstract
PURPOSE The involvement of the orexin system in the physiopathology of insomnia has been rapidly increasing in understanding. In this sense, daridorexant was the third orexin receptor antagonist approved by the FDA in January 2022. This review aims to summarize the chemistry, pharmacodynamics, pharmacokinetics, efficacy, safety, and tolerability profile of daridorexant for the treatment of insomnia disorder. METHODS We performed a review of daridorexant for the treatment of insomnia disorder. The search was carried out in Medline via PubMed, Embase, and clinical trials, up to March 2022. RESULTS Daridorexant 25 and 50 mg had more significant improvement for the wake after sleep onset (WASO), latency to persistent sleep (LPS), and subjective total sleep time (sTST) than placebo. In addition, daridorexant 50 mg was better for Insomnia Daytime Symptoms and Impacts Questionnaire (IDSIQ) than placebo. The most common adverse events were nasopharyngitis and headache. CONCLUSION Daridorexant was efficacious and safe. Studies that evaluate the long-term safety and compare daridorexant with benzodiazepines, benzodiazepine receptor agonists, sedative antidepressants, and other orexin receptor antagonists are required.
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Affiliation(s)
- Jéssica Barreto Ribeiro Dos Santos
- Health Technology Assessment and Economy Group, Center for Exact, Natural and Health Sciences, Federal University of Espírito Santo, Alto Universitário S/N, Guararema, Alegre, Espírito Santo, 29500-000, Brazil
| | - Michael Ruberson Ribeiro da Silva
- Health Technology Assessment and Economy Group, Center for Exact, Natural and Health Sciences, Federal University of Espírito Santo, Alto Universitário S/N, Guararema, Alegre, Espírito Santo, 29500-000, Brazil.
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20
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Saitoh T, Amezawa M, Horiuchi J, Nagumo Y, Yamamoto N, Kutsumura N, Ohshita R, Tokuda A, Irukayama-Tomobe Y, Ogawa Y, Ishikawa Y, Hasegawa E, Sakurai T, Uchida Y, Sato T, Gouda H, Tanimura R, Yanagisawa M, Nagase H. Discovery of novel orexin receptor antagonists using a 1,3,5-trioxazatriquinane bearing multiple effective residues (TriMER) library. Eur J Med Chem 2022; 240:114505. [DOI: 10.1016/j.ejmech.2022.114505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 05/19/2022] [Accepted: 05/27/2022] [Indexed: 11/30/2022]
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21
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Yin J, Kang Y, McGrath AP, Chapman K, Sjodt M, Kimura E, Okabe A, Koike T, Miyanohana Y, Shimizu Y, Rallabandi R, Lian P, Bai X, Flinspach M, De Brabander JK, Rosenbaum DM. Molecular mechanism of the wake-promoting agent TAK-925. Nat Commun 2022; 13:2902. [PMID: 35614071 PMCID: PMC9133036 DOI: 10.1038/s41467-022-30601-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 05/05/2022] [Indexed: 11/30/2022] Open
Abstract
The OX2 orexin receptor (OX2R) is a highly expressed G protein-coupled receptor (GPCR) in the brain that regulates wakefulness and circadian rhythms in humans. Antagonism of OX2R is a proven therapeutic strategy for insomnia drugs, and agonism of OX2R is a potentially powerful approach for narcolepsy type 1, which is characterized by the death of orexinergic neurons. Until recently, agonism of OX2R had been considered 'undruggable.' We harness cryo-electron microscopy of OX2R-G protein complexes to determine how the first clinically tested OX2R agonist TAK-925 can activate OX2R in a highly selective manner. Two structures of TAK-925-bound OX2R with either a Gq mimetic or Gi reveal that TAK-925 binds at the same site occupied by antagonists, yet interacts with the transmembrane helices to trigger activating microswitches. Our structural and mutagenesis data show that TAK-925's selectivity is mediated by subtle differences between OX1 and OX2 receptor subtypes at the orthosteric pocket. Finally, differences in the polarity of interactions at the G protein binding interfaces help to rationalize OX2R's coupling selectivity for Gq signaling. The mechanisms of TAK-925's binding, activation, and selectivity presented herein will aid in understanding the efficacy of small molecule OX2R agonists for narcolepsy and other circadian disorders.
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Affiliation(s)
- Jie Yin
- Department of Biophysics, The University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX, 75390, USA
- Chinese Institute for Brain Research, No. 26 Science Park Road, Zhongguancun Life Science Park, Changping District, Beijing, China
| | - Yanyong Kang
- Takeda Development Center Americas, Inc, 9625 Towne Centre Drive, San Diego, CA, 92121, USA
| | - Aaron P McGrath
- Takeda Development Center Americas, Inc, 9625 Towne Centre Drive, San Diego, CA, 92121, USA
| | - Karen Chapman
- Department of Biophysics, The University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX, 75390, USA
| | - Megan Sjodt
- Takeda Development Center Americas, Inc, 9625 Towne Centre Drive, San Diego, CA, 92121, USA
| | - Eiji Kimura
- Takeda Pharmaceutical Company Ltd., 26-1 Muraoka-Higashi, 2-Chome, Fujisawa, Kanagawa, 251-8555, Japan
| | - Atsutoshi Okabe
- Takeda Pharmaceutical Company Ltd., 26-1 Muraoka-Higashi, 2-Chome, Fujisawa, Kanagawa, 251-8555, Japan
| | - Tatsuki Koike
- Takeda Pharmaceutical Company Ltd., 26-1 Muraoka-Higashi, 2-Chome, Fujisawa, Kanagawa, 251-8555, Japan
| | - Yuhei Miyanohana
- Takeda Pharmaceutical Company Ltd., 26-1 Muraoka-Higashi, 2-Chome, Fujisawa, Kanagawa, 251-8555, Japan
| | - Yuji Shimizu
- Takeda Pharmaceutical Company Ltd., 26-1 Muraoka-Higashi, 2-Chome, Fujisawa, Kanagawa, 251-8555, Japan
| | - Rameshu Rallabandi
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Peng Lian
- BioHPC at the Lyda Hill Department of Bioinformatics, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Xiaochen Bai
- Department of Biophysics, The University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX, 75390, USA
| | - Mack Flinspach
- Takeda Development Center Americas, Inc, 9625 Towne Centre Drive, San Diego, CA, 92121, USA.
| | - Jef K De Brabander
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
| | - Daniel M Rosenbaum
- Department of Biophysics, The University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX, 75390, USA.
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
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22
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Liolios C, Patsis C, Lambrinidis G, Tzortzini E, Roscher M, Bauder-Wüst U, Kolocouris A, Kopka K. Investigation of Tumor Cells and Receptor-Ligand Simulation Models for the Development of PET Imaging Probes Targeting PSMA and GRPR and a Possible Crosstalk between the Two Receptors. Mol Pharm 2022; 19:2231-2247. [PMID: 35467350 DOI: 10.1021/acs.molpharmaceut.2c00070] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Prostate-specific membrane antigen (PSMA) and gastrin-releasing peptide receptor (GRPR) have both been used in nuclear medicine as targets for molecular imaging and therapy of prostate (PCa) and breast cancer (BCa). Three bioconjugate probes, the PSMA specific: [68Ga]Ga-1, ((HBED-CC)-Ahx-Lys-NH-CO-NH Glu or PSMA-11), the GRPR specific: [68Ga]Ga-2, ((HBED-CC)-4-amino-1-carboxymethyl piperidine-[D-Phe6, Sta13]BN(6-14), a bombesin (BN) analogue), and 3 (the BN analogue: 4-amino-1-carboxymethyl piperidine-[(R)-Phe6, Sta13]BN(6-14) connected with the fluorescent dye, BDP-FL), were synthesized and tested in vitro with PCa and BCa cell lines, more specifically, with PCa cells, PC-3 and LNCaP, with BCa cells, T47D, MDA-MB-231, and with the in-house created PSMA-overexpressing PC-3(PSMA), T47D(PSMA), and MDA-MB-231(PSMA). In addition, biomolecular simulations were conducted on the association of 1 and 2 with PSMA and GRPR. The PSMA overexpression resulted in an increase of cell-bound radioligand [68Ga]Ga-1 (PSMA) for PCa and BCa cells and also of [68Ga]Ga-2 (GRPR), especially in those cell lines already expressing GRPR. The results were confirmed by fluorescence-activated cell sorting with a PE-labeled PSMA-specific antibody and the fluorescence tracer 3. The docking calculations and molecular dynamics simulations showed how 1 enters the PSMA funnel region and how pharmacophore Glu-urea-Lys interacts with the arginine patch, the S1', and S1 subpockets by forming hydrogen and van der Waals bonds. The chelating moiety of 1, that is, HBED-CC, forms additional stabilizing hydrogen bonding and van der Waals interactions in the arene-binding site. Ligand 2 is diving into the GRPR transmembrane (TM) helical cavity, thereby forming hydrogen bonds through its amidated end, water-mediated hydrogen bonds, and π-π interactions. Our results provide valuable information regarding the molecular mechanisms involved in the interactions of 1 and 2 with PSMA and GRPR, which might be useful for the diagnostic imaging and therapy of PCa and BCa.
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Affiliation(s)
- Christos Liolios
- Division of Radiopharmaceutical Chemistry, German Cancer Research Centre (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.,Radiochemical Studies Laboratory, INRASTES, N.C.S.R. "Demokritos", Agia Paraskevi Attikis, 15310 Athens, Greece.,Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens (NKUA), Panepistimioupolis-Zografou, 15771 Athens, Greece
| | - Christos Patsis
- Division of Cell Plasticity and Epigenetic Remodelling, German Cancer Research Centre (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.,Department of Translational Oncology, German Cancer Research Centre (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - George Lambrinidis
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens (NKUA), Panepistimioupolis-Zografou, 15771 Athens, Greece
| | - Efpraxia Tzortzini
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens (NKUA), Panepistimioupolis-Zografou, 15771 Athens, Greece
| | - Mareike Roscher
- Division of Radiopharmaceutical Chemistry, German Cancer Research Centre (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Ulrike Bauder-Wüst
- Division of Radiopharmaceutical Chemistry, German Cancer Research Centre (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Antonios Kolocouris
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens (NKUA), Panepistimioupolis-Zografou, 15771 Athens, Greece
| | - Klaus Kopka
- Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Bautzner Landstraße 400, 01328 Dresden, Germany.,Faculty of Chemistry and Food Chemistry, School of Science, Technical University Dresden, Lebensmittelchemie Chemiegebäude, Raum 413 Bergstr. 66, 01069 Dresden, Germany
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Zhao H. Modulating Conformational Preferences by Allylic Strain toward Improved Physical Properties and Binding Interactions. ACS OMEGA 2022; 7:9080-9085. [PMID: 35309473 PMCID: PMC8928487 DOI: 10.1021/acsomega.2c00510] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 02/25/2022] [Indexed: 06/09/2023]
Abstract
The preference of the axial over the equatorial orientation of 2-substitutent for both phenyl-1-piperidines and N-acylpiperidines is studied at the M06-2X level of theory. For phenyl-1-piperidines, the axial 2-substituent is modestly favored over the equatorial one. In contrast, the pseudoallylic strain in N-acylpiperidines dictates the axial orientation of 2-substituent with a ΔG up to -3.2 kcal/mol. The calculations agree well with the statistics from both the Cambridge Structural Database of small-molecule organic crystal structures and the Protein Data Bank. The equilibrium between the twist-boat and chair conformations for N-acylpiperidines with a 2-substituent was further investigated. The twist-boat conformation is found to be around 1.5 kcal/mol less favorable. Finally, the three-dimensionality in shape resulting from minimization of the pseudoallylic strain is characterized, and its implication in protein-ligand interactions is briefly reviewed.
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Structural basis of neuropeptide Y signaling through Y1 receptor. Nat Commun 2022; 13:853. [PMID: 35165283 PMCID: PMC8844075 DOI: 10.1038/s41467-022-28510-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 01/26/2022] [Indexed: 01/07/2023] Open
Abstract
AbstractNeuropeptide Y (NPY) is highly abundant in the brain and involved in various physiological processes related to food intake and anxiety, as well as human diseases such as obesity and cancer. However, the molecular details of the interactions between NPY and its receptors are poorly understood. Here, we report a cryo-electron microscopy structure of the NPY-bound neuropeptide Y1 receptor (Y1R) in complex with Gi1 protein. The NPY C-terminal segment forming the extended conformation binds deep into the Y1R transmembrane core, where the amidated C-terminal residue Y36 of NPY is located at the base of the ligand-binding pocket. Furthermore, the helical region and two N-terminal residues of NPY interact with Y1R extracellular loops, contributing to the high affinity of NPY for Y1R. The structural analysis of NPY-bound Y1R and mutagenesis studies provide molecular insights into the activation mechanism of Y1R upon NPY binding.
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Clinical, Genetic and Functional Characterization of a Novel AVPR2 Missense Mutation in a Woman with X-Linked Recessive Nephrogenic Diabetes Insipidus. J Pers Med 2022; 12:jpm12010118. [PMID: 35055433 PMCID: PMC8779739 DOI: 10.3390/jpm12010118] [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: 12/08/2021] [Revised: 12/27/2021] [Accepted: 01/05/2022] [Indexed: 11/28/2022] Open
Abstract
Nephrogenic diabetes insipidus (NDI) is a rare disorder characterized by renal unresponsiveness to the hormone vasopressin, leading to excretion of large volumes of diluted urine. Mutations in the arginine vasopressin receptor-2 (AVPR2) gene cause congenital NDI and have an X-linked recessive inheritance. The disorder affects almost exclusively male family members, but female carriers occasionally present partial phenotypes due to skewed inactivation of the X-chromosome. Here, we report a rare case of a woman affected with X-linked recessive NDI, presenting an average urinary output of 12 L/day. Clinical and biochemical studies showed incomplete responses to water deprivation and vasopressin stimulation tests. Genetic analyses revealed a novel heterozygous missense mutation (c.493G > C, p.Ala165Pro) in the AVPR2 gene. Using a combination of in-silico protein modeling with human cellular models and molecular phenotyping, we provide functional evidence for phenotypic effects. The mutation destabilizes the helical structure of the AVPR2 transmembrane domains and disrupts its plasma membrane localization and downstream intracellular signaling pathways upon activation with its agonist vasopressin. These defects lead to deficient aquaporin 2 (AQP2) membrane translocation, explaining the inability to concentrate urine in this patient.
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Lessel U, Ferrara M, Heine N, Marelli C, Carrettoni L, Pfau R, Schmidt E, Riether D. Identification of Highly Selective Orexin 1 Receptor Antagonists Driven by Structure-Based Design. J Chem Inf Model 2021; 61:5893-5905. [PMID: 34817173 DOI: 10.1021/acs.jcim.1c01055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
OX1 receptor antagonists are of interest to treat, for example, substance abuse disorders, personality disorders, eating disorders, or anxiety-related disorders. However, known dual OX1/OX2 receptor antagonists are not suitable due to their sleep-inducing effects; therefore, we were interested in identifying a highly OX1 selective antagonist with a sufficient window to OX2-mediated effects. Herein, we describe the design of highly selective OX1 receptor antagonists driven by the X-ray structure of OX1 with suvorexant, a dual OX1/OX2 receptor antagonist. Moderately selective OX1 antagonists comprising a [2.2.1]-bicyclic scaffold served as our starting point. Based on our binding mode hypothesis, we postulated which part of the scaffold points toward one of the regions where the two binding pockets differ. Structural changes in this part resulted in a modified core with higher inherent selectivity compared to the [2.2.1]-bicyclic template. The structure-based design, synthesis, and hit-to-lead evaluation of this novel OX1 receptor-selective scaffold are discussed herein.
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Affiliation(s)
- Uta Lessel
- Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Strasse 65, 88397 Biberach an der Riss, Germany
| | - Marco Ferrara
- Boehringer Ingelheim Research Italia S.a.s. di BI IT S.r.l., Via Giovanni Lorenzini 8, 20139 Milano, MI, Italy
| | - Niklas Heine
- Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Strasse 65, 88397 Biberach an der Riss, Germany
| | - Chiara Marelli
- Boehringer Ingelheim Research Italia S.a.s. di BI IT S.r.l., Via Giovanni Lorenzini 8, 20139 Milano, MI, Italy
| | - Laura Carrettoni
- Boehringer Ingelheim Research Italia S.a.s. di BI IT S.r.l., Via Giovanni Lorenzini 8, 20139 Milano, MI, Italy
| | - Roland Pfau
- Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Strasse 65, 88397 Biberach an der Riss, Germany
| | - Esther Schmidt
- Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Strasse 65, 88397 Biberach an der Riss, Germany
| | - Doris Riether
- Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Strasse 65, 88397 Biberach an der Riss, Germany
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Coleman P, de Lecea L, Gotter A, Hagan J, Hoyer D, Kilduff T, Kukkonen JP, Porter R, Renger J, Siegel JM, Sutcliffe G, Upton N, Winrow CJ. Orexin receptors in GtoPdb v.2021.3. IUPHAR/BPS GUIDE TO PHARMACOLOGY CITE 2021; 2021. [PMID: 34927075 DOI: 10.2218/gtopdb/f51/2021.3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Orexin receptors (nomenclature as agreed by the NC-IUPHAR Subcommittee on Orexin receptors [42]) are activated by the endogenous polypeptides orexin-A and orexin-B (also known as hypocretin-1 and -2; 33 and 28 aa) derived from a common precursor, preproorexin or orexin precursor, by proteolytic cleavage and some typical peptide modifications [109]. Currently the only orexin receptor ligands in clinical use are suvorexant and lemborexant, which are used as hypnotics. Orexin receptor crystal structures have been solved [134, 133, 54, 117, 46].
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Ballante F, Kooistra AJ, Kampen S, de Graaf C, Carlsson J. Structure-Based Virtual Screening for Ligands of G Protein-Coupled Receptors: What Can Molecular Docking Do for You? Pharmacol Rev 2021; 73:527-565. [PMID: 34907092 DOI: 10.1124/pharmrev.120.000246] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
G protein-coupled receptors (GPCRs) constitute the largest family of membrane proteins in the human genome and are important therapeutic targets. During the last decade, the number of atomic-resolution structures of GPCRs has increased rapidly, providing insights into drug binding at the molecular level. These breakthroughs have created excitement regarding the potential of using structural information in ligand design and initiated a new era of rational drug discovery for GPCRs. The molecular docking method is now widely applied to model the three-dimensional structures of GPCR-ligand complexes and screen for chemical probes in large compound libraries. In this review article, we first summarize the current structural coverage of the GPCR superfamily and the understanding of receptor-ligand interactions at atomic resolution. We then present the general workflow of structure-based virtual screening and strategies to discover GPCR ligands in chemical libraries. We assess the state of the art of this research field by summarizing prospective applications of virtual screening based on experimental structures. Strategies to identify compounds with specific efficacy and selectivity profiles are discussed, illustrating the opportunities and limitations of the molecular docking method. Our overview shows that structure-based virtual screening can discover novel leads and will be essential in pursuing the next generation of GPCR drugs. SIGNIFICANCE STATEMENT: Extraordinary advances in the structural biology of G protein-coupled receptors have revealed the molecular details of ligand recognition by this large family of therapeutic targets, providing novel avenues for rational drug design. Structure-based docking is an efficient computational approach to identify novel chemical probes from large compound libraries, which has the potential to accelerate the development of drug candidates.
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Affiliation(s)
- Flavio Ballante
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden (F.B., S.K., J.C.); Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark (A.J.K.); and Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge, United Kingdom (C.d.G.)
| | - Albert J Kooistra
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden (F.B., S.K., J.C.); Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark (A.J.K.); and Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge, United Kingdom (C.d.G.)
| | - Stefanie Kampen
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden (F.B., S.K., J.C.); Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark (A.J.K.); and Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge, United Kingdom (C.d.G.)
| | - Chris de Graaf
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden (F.B., S.K., J.C.); Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark (A.J.K.); and Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge, United Kingdom (C.d.G.)
| | - Jens Carlsson
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden (F.B., S.K., J.C.); Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark (A.J.K.); and Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge, United Kingdom (C.d.G.)
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Yokoi S, Mitsutake A. Characteristic structural difference between inactive and active states of orexin 2 receptor determined using molecular dynamics simulations. Biophys Rev 2021; 14:221-231. [DOI: 10.1007/s12551-021-00862-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 10/20/2021] [Indexed: 12/12/2022] Open
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30
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The Novel Application of Geometric Morphometrics with Principal Component Analysis to Existing G Protein-Coupled Receptor (GPCR) Structures. Pharmaceuticals (Basel) 2021; 14:ph14100953. [PMID: 34681177 PMCID: PMC8541025 DOI: 10.3390/ph14100953] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/17/2021] [Accepted: 09/19/2021] [Indexed: 12/24/2022] Open
Abstract
The G protein-coupled receptor (GPCR) superfamily is a large group of membrane proteins which, because of their vast involvement in cell signalling pathways, are implicated in a plethora of disease states and are therefore considered to be key drug targets. Despite advances in techniques to study these receptors, current prophylaxis is often limited due to the challenging nature of their dynamic, complex structures. Greater knowledge and understanding of their intricate structural rearrangements will therefore undoubtedly aid structure-based drug design against GPCRs. Disciplines such as anthropology and palaeontology often use geometric morphometrics to measure variation between shapes and we have therefore applied this technique to analyse GPCR structures in a three-dimensional manner, using principal component analysis. Our aim was to create a novel system able to discriminate between GPCR structures and discover variation between them, correlated with a variety of receptor characteristics. This was conducted by assessing shape changes at the extra- and intracellular faces of the transmembrane helix bundle, analysing the XYZ coordinates of the amino acids at those positions. We have demonstrated that GPCR structures can be classified based on characteristics such as activation state, bound ligands and fusion proteins, with the most significant results focussed at the intracellular face. Conversely, our analyses provide evidence that thermostabilising mutations do not cause significant differences when compared to non-mutated GPCRs. We believe that this is the first time geometric morphometrics has been applied to membrane proteins on this scale, and believe it can be used as a future tool in sense-checking newly resolved structures and planning experimental design.
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31
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Zou R, Wang X, Li S, Chan HCS, Vogel H, Yuan S. The role of metal ions in G protein‐coupled receptor signalling and drug discovery. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2021. [DOI: 10.1002/wcms.1565] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Rongfeng Zou
- Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences Shenzhen China
- AlphaMol Science Ltd Shenzhen China
| | - Xueying Wang
- Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences Shenzhen China
| | - Shu Li
- Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences Shenzhen China
| | - H. C. Stephen Chan
- Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences Shenzhen China
| | - Horst Vogel
- Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences Shenzhen China
- AlphaMol Science Ltd Shenzhen China
- Ecole Polytechnique Fédérale de Lausanne (EPFL) Lausanne Switzerland
| | - Shuguang Yuan
- Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences Shenzhen China
- AlphaMol Science Ltd Shenzhen China
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Yokoi S, Mitsutake A. Molecular Dynamics Simulations for the Determination of the Characteristic Structural Differences between Inactive and Active States of Wild Type and Mutants of the Orexin2 Receptor. J Phys Chem B 2021; 125:4286-4298. [PMID: 33885321 DOI: 10.1021/acs.jpcb.0c10985] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The orexin2 receptor (OX2R), which is classified as a class A G protein-coupled receptor (GPCR), is the target of our study. We performed over 20 several-microsecond-scale molecular dynamics simulations of the wild type and mutants of OX2R to extract the characteristics of the structural changes taking place in the active state. We introduced mutations that exhibited the stable inactive state and the constitutively active state in class A GPCRs. In these simulations, significant characteristic structural changes were observed in the V3096.40Y mutant, which corresponded to a constitutively active mutant. These conformational changes include the outward movement of the transmembrane helix 6 (TM6) and the inward movement of TM7, which are common structural changes in the activation of GPCRs. In addition, we extracted a suitable index for the quantitative evaluation of the active and inactive states of GPCRs, namely, the inter-atomic distance of Cα atoms between x(3.46) and Y(7.53). The structures of the inactive and active states solved by X-ray crystallography and cryo-electron microscopy can be classified using the inter-atomic distance. Furthermore, we clarified that the inward movement of TM7 requires the swapping of M3056.36 on TM6 and L3677.56 on TM7. Finally, we discussed the structural advantages of TM7 inward movement for GPCR activation.
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Affiliation(s)
- Shun Yokoi
- Department of Physics, School of Science and Technology, Meiji University, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, Kanagawa 214-8571, Japan
| | - Ayori Mitsutake
- Department of Physics, School of Science and Technology, Meiji University, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, Kanagawa 214-8571, Japan
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Bauer MR, Di Fruscia P, Lucas SCC, Michaelides IN, Nelson JE, Storer RI, Whitehurst BC. Put a ring on it: application of small aliphatic rings in medicinal chemistry. RSC Med Chem 2021; 12:448-471. [PMID: 33937776 PMCID: PMC8083977 DOI: 10.1039/d0md00370k] [Citation(s) in RCA: 143] [Impact Index Per Article: 47.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 12/18/2020] [Indexed: 12/15/2022] Open
Abstract
Aliphatic three- and four-membered rings including cyclopropanes, cyclobutanes, oxetanes, azetidines and bicyclo[1.1.1]pentanes have been increasingly exploited in medicinal chemistry for their beneficial physicochemical properties and applications as functional group bioisosteres. This review provides a historical perspective and comparative up to date overview of commonly applied small rings, exemplifying key principles with recent literature examples. In addition to describing the merits and advantages of each ring system, potential hazards and liabilities are also illustrated and explained, including any significant chemical or metabolic stability and toxicity risks.
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Affiliation(s)
- Matthias R Bauer
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca Cambridge UK
| | - Paolo Di Fruscia
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca Cambridge UK
| | - Simon C C Lucas
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca Cambridge UK
| | | | - Jennifer E Nelson
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca Cambridge UK
| | - R Ian Storer
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca Cambridge UK
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Albanese V, Ruzza C, Marzola E, Bernardi T, Fabbri M, Fantinati A, Trapella C, Reinscheid RK, Ferrari F, Sturaro C, Calò G, Amendola G, Cosconati S, Pacifico S, Guerrini R, Preti D. Structure-Activity Relationship Studies on Oxazolo[3,4- a]pyrazine Derivatives Leading to the Discovery of a Novel Neuropeptide S Receptor Antagonist with Potent In Vivo Activity. J Med Chem 2021; 64:4089-4108. [PMID: 33733768 PMCID: PMC8041306 DOI: 10.1021/acs.jmedchem.0c02223] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Neuropeptide S modulates important neurobiological functions including locomotion, anxiety, and drug abuse through interaction with its G protein-coupled receptor known as neuropeptide S receptor (NPSR). NPSR antagonists are potentially useful for the treatment of substance abuse disorders against which there is an urgent need for new effective therapeutic approaches. Potent NPSR antagonists in vitro have been discovered which, however, require further optimization of their in vivo pharmacological profile. This work describes a new series of NPSR antagonists of the oxazolo[3,4-a]pyrazine class. The guanidine derivative 16 exhibited nanomolar activity in vitro and 5-fold improved potency in vivo compared to SHA-68, a reference pharmacological tool in this field. Compound 16 can be considered a new tool for research studies on the translational potential of the NPSergic system. An in-depth molecular modeling investigation was also performed to gain new insights into the observed structure-activity relationships and provide an updated model of ligand/NPSR interactions.
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Affiliation(s)
- Valentina Albanese
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Via Luigi Borsari 46, 44121 Ferrara, Italy
| | - Chiara Ruzza
- Department of Neuroscience and Rehabilitation, Section of Pharmacology, University of Ferrara, Via Fossato di Mortara 17/19, 44121 Ferrara, Italy
- LTTA Laboratory for Advanced Therapies, Technopole of Ferrara, 44121 Ferrara, Italy
| | - Erika Marzola
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Via Luigi Borsari 46, 44121 Ferrara, Italy
| | - Tatiana Bernardi
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Via Luigi Borsari 46, 44121 Ferrara, Italy
| | - Martina Fabbri
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Via Luigi Borsari 46, 44121 Ferrara, Italy
| | - Anna Fantinati
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Via Luigi Borsari 46, 44121 Ferrara, Italy
| | - Claudio Trapella
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Via Luigi Borsari 46, 44121 Ferrara, Italy
- LTTA Laboratory for Advanced Therapies, Technopole of Ferrara, 44121 Ferrara, Italy
| | - Rainer K Reinscheid
- Institute of Pharmacology and Toxicology, Jena University Hospital, Friedrich Schiller University, 07747 Jena, Germany
- Institute of Physiology I, University Hospital Münster, University of Münster, 48149 Münster, Germany
| | - Federica Ferrari
- Department of Neuroscience and Rehabilitation, Section of Pharmacology, University of Ferrara, Via Fossato di Mortara 17/19, 44121 Ferrara, Italy
| | - Chiara Sturaro
- Department of Neuroscience and Rehabilitation, Section of Pharmacology, University of Ferrara, Via Fossato di Mortara 17/19, 44121 Ferrara, Italy
| | - Girolamo Calò
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Largo Meneghetti, 2, 35131 Padova, Italy
| | - Giorgio Amendola
- "DiSTABiF", Università della Campania "Luigi Vanvitelli", Via Vivaldi 43, 81100 Caserta, Italy
| | - Sandro Cosconati
- "DiSTABiF", Università della Campania "Luigi Vanvitelli", Via Vivaldi 43, 81100 Caserta, Italy
| | - Salvatore Pacifico
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Via Luigi Borsari 46, 44121 Ferrara, Italy
| | - Remo Guerrini
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Via Luigi Borsari 46, 44121 Ferrara, Italy
- LTTA Laboratory for Advanced Therapies, Technopole of Ferrara, 44121 Ferrara, Italy
| | - Delia Preti
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Via Luigi Borsari 46, 44121 Ferrara, Italy
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Structures of active-state orexin receptor 2 rationalize peptide and small-molecule agonist recognition and receptor activation. Nat Commun 2021; 12:815. [PMID: 33547286 PMCID: PMC7864924 DOI: 10.1038/s41467-021-21087-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 01/05/2021] [Indexed: 02/07/2023] Open
Abstract
Narcolepsy type 1 (NT1) is a chronic neurological disorder that impairs the brain’s ability to control sleep-wake cycles. Current therapies are limited to the management of symptoms with modest effectiveness and substantial adverse effects. Agonists of the orexin receptor 2 (OX2R) have shown promise as novel therapeutics that directly target the pathophysiology of the disease. However, identification of drug-like OX2R agonists has proven difficult. Here we report cryo-electron microscopy structures of active-state OX2R bound to an endogenous peptide agonist and a small-molecule agonist. The extended carboxy-terminal segment of the peptide reaches into the core of OX2R to stabilize an active conformation, while the small-molecule agonist binds deep inside the orthosteric pocket, making similar key interactions. Comparison with antagonist-bound OX2R suggests a molecular mechanism that rationalizes both receptor activation and inhibition. Our results enable structure-based discovery of therapeutic orexin agonists for the treatment of NT1 and other hypersomnia disorders. Agonists of the orexin receptor 2 (OX2R) show promise in the treatment of narcolepsy. Cryo-EM structures of active-state OX2R bound to an endogenous peptide agonist and a small-molecule agonist suggest a molecular mechanism that rationalizes both receptor activation and inhibition.
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Tiss A, Ben Boubaker R, Henrion D, Guissouma H, Chabbert M. Homology Modeling of Class A G-Protein-Coupled Receptors in the Age of the Structure Boom. Methods Mol Biol 2021; 2315:73-97. [PMID: 34302671 DOI: 10.1007/978-1-0716-1468-6_5] [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: 12/31/2022]
Abstract
With 700 members, G protein-coupled receptors (GPCRs) of the rhodopsin family (class A) form the largest membrane receptor family in humans and are the target of about 30% of presently available pharmaceutical drugs. The recent boom in GPCR structures led to the structural resolution of 57 unique receptors in different states (39 receptors in inactive state only, 2 receptors in active state only and 16 receptors in different activation states). In spite of these tremendous advances, most computational studies on GPCRs, including molecular dynamics simulations, virtual screening and drug design, rely on GPCR models obtained by homology modeling. In this protocol, we detail the different steps of homology modeling with the MODELLER software, from template selection to model evaluation. The present structure boom provides closely related templates for most receptors. If, in these templates, some of the loops are not resolved, in most cases, the numerous available structures enable to find loop templates with similar length for equivalent loops. However, simultaneously, the large number of putative templates leads to model ambiguities that may require additional information based on multiple sequence alignments or molecular dynamics simulations to be resolved. Using the modeling of the human bradykinin receptor B1 as a case study, we show how several templates are managed by MODELLER, and how the choice of template(s) and of template fragments can improve the quality of the models. We also give examples of how additional information and tools help the user to resolve ambiguities in GPCR modeling.
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Affiliation(s)
- Asma Tiss
- UMR CNRS 6015 - INSERM 1083, Laboratoire MITOVASC, Université d'Angers, Angers, France.,Laboratoire de Génétique, Immunologie et Pathologies Humaines, Département de Biologie, Faculté des Sciences de Tunis, Université de Tunis El Manar, Tunis, Tunisie
| | - Rym Ben Boubaker
- UMR CNRS 6015 - INSERM 1083, Laboratoire MITOVASC, Université d'Angers, Angers, France
| | - Daniel Henrion
- UMR CNRS 6015 - INSERM 1083, Laboratoire MITOVASC, Université d'Angers, Angers, France
| | - Hajer Guissouma
- Laboratoire de Génétique, Immunologie et Pathologies Humaines, Département de Biologie, Faculté des Sciences de Tunis, Université de Tunis El Manar, Tunis, Tunisie
| | - Marie Chabbert
- UMR CNRS 6015 - INSERM 1083, Laboratoire MITOVASC, Université d'Angers, Angers, France.
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Krull F, Hirschfeld M, Wemheuer WE, Brenig B. Frameshift Variant in Novel Adenosine-A1-Receptor Homolog Associated With Bovine Spastic Syndrome/Late-Onset Bovine Spastic Paresis in Holstein Sires. Front Genet 2020; 11:591794. [PMID: 33329738 PMCID: PMC7734149 DOI: 10.3389/fgene.2020.591794] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 10/26/2020] [Indexed: 11/13/2022] Open
Abstract
Since their first description almost 100 years ago, bovine spastic paresis (BSP) and bovine spastic syndrome (BSS) are assumed to be inherited neuronal-progressive diseases in cattle. Affected animals are characterized by (frequent) spasms primarily located in the hind limbs, accompanied by severe pain symptoms and reduced vigor, thus initiating premature slaughter or euthanasia. Due to the late onset of BSP and BSS and the massively decreased lifespan of modern cattle, the importance of these diseases is underestimated. In the present study, BSP/BSS-affected German Holstein breeding sires from artificial insemination centers were collected and pedigree analysis, genome-wide association studies, whole genome resequencing, protein-protein interaction network analysis, and protein-homology modeling were performed to elucidate the genetic background. The analysis of 46 affected and 213 control cattle revealed four significantly associated positions on chromosome 15 (BTA15), i.e., AC_000172.1:g.83465449A>G (-log10P = 19.17), AC_000172.1:g.81871849C>T (-log10P = 8.31), AC_000172.1:g.81872621A>T (-log10P = 6.81), and AC_000172.1:g.81872661G>C (-log10P = 6.42). Two additional loci were significantly associated located on BTA8 and BTA19, i.e., AC_000165.1:g.71177788T>C and AC_000176.1:g.30140977T>G, respectively. Whole genome resequencing of five affected individuals and six unaffected relatives (two fathers, two mothers, a half sibling, and a full sibling) belonging to three different not directly related families was performed. After filtering, a homozygous loss of function variant was identified in the affected cattle, causing a frameshift in the so far unknown gene locus LOC100848076 encoding an adenosine-A1-receptor homolog. An allele frequency of the variant of 0.74 was determined in 3,093 samples of the 1000 Bull Genomes Project.
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Affiliation(s)
- Frederik Krull
- Department of Animal Sciences, Faculty of Agricultural Sciences, Institute of Veterinary Medicine, University of Göttingen, Göttingen, Germany
| | - Marc Hirschfeld
- Department of Animal Sciences, Faculty of Agricultural Sciences, Institute of Veterinary Medicine, University of Göttingen, Göttingen, Germany
| | - Wilhelm Ewald Wemheuer
- Department of Animal Sciences, Faculty of Agricultural Sciences, Institute of Veterinary Medicine, University of Göttingen, Göttingen, Germany
| | - Bertram Brenig
- Department of Animal Sciences, Faculty of Agricultural Sciences, Institute of Veterinary Medicine, University of Göttingen, Göttingen, Germany
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38
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Membrane protein crystallography in the era of modern structural biology. Biochem Soc Trans 2020; 48:2505-2524. [DOI: 10.1042/bst20200066] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 10/15/2020] [Accepted: 10/16/2020] [Indexed: 02/07/2023]
Abstract
The aim of structural biology has been always the study of biological macromolecules structures and their mechanistic behaviour at molecular level. To achieve its goal, multiple biophysical methods and approaches have become part of the structural biology toolbox. Considered as one of the pillars of structural biology, X-ray crystallography has been the most successful method for solving three-dimensional protein structures at atomic level to date. It is however limited by the success in obtaining well-ordered protein crystals that diffract at high resolution. This is especially true for challenging targets such as membrane proteins (MPs). Understanding structure-function relationships of MPs at the biochemical level is vital for medicine and drug discovery as they play critical roles in many cellular processes. Though difficult, structure determination of MPs by X-ray crystallography has significantly improved in the last two decades, mainly due to many relevant technological and methodological developments. Today, numerous MP crystal structures have been solved, revealing many of their mechanisms of action. Yet the field of structural biology has also been through significant technological breakthroughs in recent years, particularly in the fields of single particle electron microscopy (cryo-EM) and X-ray free electron lasers (XFELs). Here we summarise the most important advancements in the field of MP crystallography and the significance of these developments in the present era of modern structural biology.
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Boss C, Gatfield J, Brotschi C, Heidmann B, Sifferlen T, von Raumer M, Schmidt G, Williams JT, Treiber A, Roch C. The Quest for the Best Dual Orexin Receptor Antagonist (Daridorexant) for the Treatment of Insomnia Disorders. ChemMedChem 2020; 15:2286-2305. [PMID: 32937014 DOI: 10.1002/cmdc.202000453] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 09/06/2020] [Indexed: 02/06/2023]
Abstract
Since its discovery in 1998, the orexin system has been of interest to the research community as a potential therapeutic target for the treatment of sleep/wake disorders, stress and anxiety disorders, addiction or eating disorders. It consists of two G protein-coupled receptors, the orexin 1 and orexin 2 receptors, and two neuropeptides with agonistic effects, the orexin A and orexin B peptides. Herein we describe our efforts leading to the identification of a promising set of dual orexin receptor antagonists (DORAs) which subsequently went through physiology-based pharmacokinetic and pharmacodynamic modelling>[1] and finally led to the selection of daridorexant, currently in phase 3 clinical trials for the treatment of insomnia disorders.
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Affiliation(s)
- Christoph Boss
- Drug Discovery and Preclinical Research & Development, Idorsia Pharmaceuticals Ltd., Hegenheimermattweg 91, 4123, Allschwil, BL, Switzerland
| | - John Gatfield
- Drug Discovery and Preclinical Research & Development, Idorsia Pharmaceuticals Ltd., Hegenheimermattweg 91, 4123, Allschwil, BL, Switzerland
| | - Christine Brotschi
- Drug Discovery and Preclinical Research & Development, Idorsia Pharmaceuticals Ltd., Hegenheimermattweg 91, 4123, Allschwil, BL, Switzerland
| | - Bibia Heidmann
- Drug Discovery and Preclinical Research & Development, Idorsia Pharmaceuticals Ltd., Hegenheimermattweg 91, 4123, Allschwil, BL, Switzerland
| | - Thierry Sifferlen
- Drug Discovery and Preclinical Research & Development, Idorsia Pharmaceuticals Ltd., Hegenheimermattweg 91, 4123, Allschwil, BL, Switzerland
| | - Markus von Raumer
- Drug Discovery and Preclinical Research & Development, Idorsia Pharmaceuticals Ltd., Hegenheimermattweg 91, 4123, Allschwil, BL, Switzerland
| | - Gunther Schmidt
- Drug Discovery and Preclinical Research & Development, Idorsia Pharmaceuticals Ltd., Hegenheimermattweg 91, 4123, Allschwil, BL, Switzerland
| | - Jodi T Williams
- Drug Discovery and Preclinical Research & Development, Idorsia Pharmaceuticals Ltd., Hegenheimermattweg 91, 4123, Allschwil, BL, Switzerland
| | - Alexander Treiber
- Drug Discovery and Preclinical Research & Development, Idorsia Pharmaceuticals Ltd., Hegenheimermattweg 91, 4123, Allschwil, BL, Switzerland
| | - Catherine Roch
- Drug Discovery and Preclinical Research & Development, Idorsia Pharmaceuticals Ltd., Hegenheimermattweg 91, 4123, Allschwil, BL, Switzerland
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40
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Préville C, Bonaventure P, Koudriakova T, Lord B, Nepomuceno D, Rizzolio M, Mani N, Coe KJ, Ndifor A, Dugovic C, Dvorak CA, Coate H, Pippel DJ, Fitzgerald A, Allison B, Lovenberg TW, Carruthers NI, Shireman BT. Substituted Azabicyclo[2.2.1]heptanes as Selective Orexin-1 Antagonists: Discovery of JNJ-54717793. ACS Med Chem Lett 2020; 11:2002-2009. [PMID: 33062185 DOI: 10.1021/acsmedchemlett.0c00085] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 04/27/2020] [Indexed: 12/30/2022] Open
Abstract
The orexin system consists of two neuropeptides (orexin-A and orexin-B) that exert their mode of action on two receptors (orexin-1 and orexin-2). While the role of the orexin-2 receptor is established as an important modulator of sleep wake states, the role of the orexin-1 receptor is believed to play a role in addiction, panic, or anxiety. In this manuscript, we describe the optimization of a nonselective substituted azabicyclo[2.2.1]heptane dual orexin receptor antagonist (DORA) into orally bioavailable, brain penetrating, selective orexin-1 receptor (OX1R) antagonists. This resulted in the discovery of our first candidate for clinical development, JNJ-54717793.
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Affiliation(s)
- Cathy Préville
- Janssen Research & Development L.L.C., 3210 Merryfield Row, San Diego, California 92121, United States
| | - Pascal Bonaventure
- Janssen Research & Development L.L.C., 3210 Merryfield Row, San Diego, California 92121, United States
| | - Tatiana Koudriakova
- Janssen Research & Development L.L.C., 3210 Merryfield Row, San Diego, California 92121, United States
| | - Brian Lord
- Janssen Research & Development L.L.C., 3210 Merryfield Row, San Diego, California 92121, United States
| | - Diane Nepomuceno
- Janssen Research & Development L.L.C., 3210 Merryfield Row, San Diego, California 92121, United States
| | - Michele Rizzolio
- Janssen Research & Development L.L.C., 3210 Merryfield Row, San Diego, California 92121, United States
| | - Neelakandha Mani
- Janssen Research & Development L.L.C., 3210 Merryfield Row, San Diego, California 92121, United States
| | - Kevin J. Coe
- Janssen Research & Development L.L.C., 3210 Merryfield Row, San Diego, California 92121, United States
| | - Anthony Ndifor
- Janssen Research & Development L.L.C., 3210 Merryfield Row, San Diego, California 92121, United States
| | - Christine Dugovic
- Janssen Research & Development L.L.C., 3210 Merryfield Row, San Diego, California 92121, United States
| | - Curt A. Dvorak
- Janssen Research & Development L.L.C., 3210 Merryfield Row, San Diego, California 92121, United States
| | - Heather Coate
- Janssen Research & Development L.L.C., 3210 Merryfield Row, San Diego, California 92121, United States
| | - Daniel J. Pippel
- Janssen Research & Development L.L.C., 3210 Merryfield Row, San Diego, California 92121, United States
| | - Anne Fitzgerald
- Janssen Research & Development L.L.C., 3210 Merryfield Row, San Diego, California 92121, United States
| | - Brett Allison
- Janssen Research & Development L.L.C., 3210 Merryfield Row, San Diego, California 92121, United States
| | - Timothy W. Lovenberg
- Janssen Research & Development L.L.C., 3210 Merryfield Row, San Diego, California 92121, United States
| | - Nicholas I. Carruthers
- Janssen Research & Development L.L.C., 3210 Merryfield Row, San Diego, California 92121, United States
| | - Brock T. Shireman
- Janssen Research & Development L.L.C., 3210 Merryfield Row, San Diego, California 92121, United States
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Liu J, Han J, Izawa K, Sato T, White S, Meanwell NA, Soloshonok VA. Cyclic tailor-made amino acids in the design of modern pharmaceuticals. Eur J Med Chem 2020; 208:112736. [PMID: 32966895 DOI: 10.1016/j.ejmech.2020.112736] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 08/03/2020] [Accepted: 08/04/2020] [Indexed: 12/15/2022]
Abstract
Tailor-made AAs are indispensable components of modern medicinal chemistry and are becoming increasingly prominent in new drugs. In fact, about 30% of small-molecule pharmaceuticals contain residues of tailor-made AAs or structurally related diamines and amino-alcohols. Cyclic tailor-made AAs present a particular value to rational structural design by virtue of their local conformational constraints and are widely used in lead optimization programs. The present review article highlights 34 compounds, all of which are derived from cyclic AAs, representing recently-approved, small-molecule pharmaceuticals as well as promising drug candidates currently in various phases of clinical study. For each compound, the discussion includes the discovery, therapeutic profile and optimized synthesis, with a focus on the preparation of cyclic tailor-made AA as the principal structural feature. The present review article is intended to serve as a reference source for organic, medicinal and process chemists along with other professionals working in the fields of drug design and pharmaceutical discovery.
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Affiliation(s)
- Jiang Liu
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Jianlin Han
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Kunisuke Izawa
- Hamari Chemicals Ltd., 1-4-29 Kunijima, Higashi-Yodogawa-ku, Osaka, 533-0024, Japan.
| | - Tatsunori Sato
- Hamari Chemicals Ltd., 1-4-29 Kunijima, Higashi-Yodogawa-ku, Osaka, 533-0024, Japan
| | - Sarah White
- Oakwood Chemical, Inc, 730 Columbia Hwy. N, Estill, SC, 29918, USA
| | - Nicholas A Meanwell
- Department of Small Molecule Drug Discovery, Bristol Myers Squibb Research and Early Development, PO Box, 4000, Princeton, NJ, 08543 4000, United States
| | - Vadim A Soloshonok
- Department of Organic Chemistry I, Faculty of Chemistry, University of the Basque Country UPV/EHU, Paseo Manuel Lardizábal 3, 20018, San Sebastián, Spain; IKERBASQUE, Basque Foundation for Science, María Díaz de Haro 3, Plaza Bizkaia, 48013, Bilbao, Spain.
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42
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Guo B, Xiu J, Shen Y, Li Q. Synthesis and biological activity evaluation of azacycloheptane sulfonamide derivatives as potential orexin receptor antagonists. RSC Adv 2020; 10:30683-30691. [PMID: 35516053 PMCID: PMC9056352 DOI: 10.1039/d0ra05068g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 08/12/2020] [Indexed: 01/09/2023] Open
Abstract
As the orexin signaling system is crucial for the regulation of the sleep/wake cycle, inhibitors of orexin-1 and orexin-2 receptors are of significant interest in the treatment of insomnia. Herein, a series of novel azacycloheptane sulfonamide derivatives were designed and synthesized, and all the compounds were evaluated as potential orexin receptor inhibitors by FLIPR Tetra calcium assay. A majority of the tested azacycloheptane sulfonamide derivatives showed OX1R and OX2R inhibitory activity. Chloro-substituted derivatives functionalized at the C5 or C6 position of the benzoxazole group exhibited better inhibitory activity for OX1R and OX2R than unsubstituted derivatives functionalized at C5 or C6. In addition, phenyl group modification had positive effects on the inhibitory activities, and an electron-withdrawing fluorine group at the ortho or meta position of the phenyl ring improved the OX2R inhibitory activity of the derivatives. This suggests that azacycloheptane sulfonamide derivatives are promising scaffolds for the development of OX1R and OX2R antagonists. Azacycloheptane sulfonamide derivatives are promising scaffolds for the development of OX1R and OX2R antagonists.![]()
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Affiliation(s)
- Bin Guo
- School of Pharmaceutical Science, Chongqing Medical University Chongqing 400016 China
| | - Jingya Xiu
- Jiangsu Nhwaluokang Pharmaceutical Research and Development Co., Ltd. Chongqing 400016 China
| | - Yi Shen
- Jiangsu Nhwaluokang Pharmaceutical Research and Development Co., Ltd. Chongqing 400016 China
| | - Qingeng Li
- School of Pharmaceutical Science, Chongqing Medical University Chongqing 400016 China
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43
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Structure-based development of a subtype-selective orexin 1 receptor antagonist. Proc Natl Acad Sci U S A 2020; 117:18059-18067. [PMID: 32669442 DOI: 10.1073/pnas.2002704117] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Orexins are neuropeptides that activate the rhodopsin-like G protein-coupled receptors OX1R and OX2R. The orexin system plays an important role in the regulation of the sleep-wake cycle and the regulation of feeding and emotions. The nonselective orexin receptor antagonist suvorexant has been the first drug on the market targeting the orexin system and is prescribed for the treatment of insomnia. Subtype-selective OX1R antagonists are valuable tools to further investigate the functions and physiological role of the OX1R in vivo and promising lead compounds for the treatment of drug addiction, anxiety, pain or obesity. Starting from the OX1R and OX2R crystal structures bound to suvorexant, we exploited a single amino acid difference in the orthosteric binding site by using molecular docking and structure-based drug design to optimize ligand interactions with the OX1R while introducing repulsive interactions with the OX2R. A newly established enantiospecific synthesis provided ligands showing up to 75-fold selectivity for the OX1R over the OX2R subtype. The structure of a new OX1R antagonist with subnanomolar affinity (JH112) was determined by crystallography in complex with the OX1R and corresponded closely to the docking-predicted geometry. JH112 exhibits high selectivity over a panel of different GPCRs, is able to cross the blood-brain barrier and acts as slowly diffusing and insurmountable antagonist for Gq protein activation and in particular β-arrestin-2 recruitment at OX1R. This study demonstrates the potential of structure-based drug design to develop more subtype-selective GPCR ligands with potentially reduced side effects and provides an attractive probe molecule and lead compound.
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Deflorian F, Perez-Benito L, Lenselink EB, Congreve M, van Vlijmen HWT, Mason JS, Graaf CD, Tresadern G. Accurate Prediction of GPCR Ligand Binding Affinity with Free Energy Perturbation. J Chem Inf Model 2020; 60:5563-5579. [PMID: 32539374 DOI: 10.1021/acs.jcim.0c00449] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The computational prediction of relative binding free energies is a crucial goal for drug discovery, and G protein-coupled receptors (GPCRs) are arguably the most important drug target class. However, they present increased complexity to model compared to soluble globular proteins. Despite breakthroughs, experimental X-ray crystal and cryo-EM structures are challenging to attain, meaning computational models of the receptor and ligand binding mode are sometimes necessary. This leads to uncertainty in understanding ligand-protein binding induced changes such as, water positioning and displacement, side chain positioning, hydrogen bond networks, and the overall structure of the hydration shell around the ligand and protein. In other words, the very elements that define structure activity relationships (SARs) and are crucial for accurate binding free energy calculations are typically more uncertain for GPCRs. In this work we use free energy perturbation (FEP) to predict the relative binding free energies for ligands of two different GPCRs. We pinpoint the key aspects for success such as the important role of key water molecules, amino acid ionization states, and the benefit of equilibration with specific ligands. Initial calculations following typical FEP setup and execution protocols delivered no correlation with experiment, but we show how results are improved in a logical and systematic way. This approach gave, in the best cases, a coefficient of determination (R2) compared with experiment in the range of 0.6-0.9 and mean unsigned errors compared to experiment of 0.6-0.7 kcal/mol. We anticipate that our findings will be applicable to other difficult-to-model protein ligand data sets and be of wide interest for the community to continue improving FE binding energy predictions.
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Affiliation(s)
- Francesca Deflorian
- Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge CB21 6DG United Kingdom
| | - Laura Perez-Benito
- Computational Chemistry, Janssen Research & Development, Janssen Pharmaceutica N. V., Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - Eelke B Lenselink
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, Leiden 2300, RA, The Netherlands
| | - Miles Congreve
- Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge CB21 6DG United Kingdom
| | - Herman W T van Vlijmen
- Computational Chemistry, Janssen Research & Development, Janssen Pharmaceutica N. V., Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - Jonathan S Mason
- Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge CB21 6DG United Kingdom
| | - Chris de Graaf
- Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge CB21 6DG United Kingdom
| | - Gary Tresadern
- Computational Chemistry, Janssen Research & Development, Janssen Pharmaceutica N. V., Turnhoutseweg 30, B-2340 Beerse, Belgium
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45
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Congreve M, de Graaf C, Swain NA, Tate CG. Impact of GPCR Structures on Drug Discovery. Cell 2020; 181:81-91. [DOI: 10.1016/j.cell.2020.03.003] [Citation(s) in RCA: 119] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 03/03/2020] [Accepted: 03/03/2020] [Indexed: 12/21/2022]
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46
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Abstract
Orexin receptors are G protein coupled receptors that may be useful targets for sleep disorders, eating disorders, or addictive behavior. Recent work shows that binding of antagonists to these receptors is complex, with strong dependence on hydrophobic hot spots and networks of water-mediated hydrogen bonds. Despite the minimal structural differences between receptor types, selectivity can be achieved in a number of different ways.
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Affiliation(s)
- D Eric Walters
- Department of Pharmaceutical Sciences, College of Pharmacy , Rosalind Franklin University of Medicine and Science , 3333 Green Bay Road , North Chicago , Illinois 60064 , United States
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