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Okamoto HH, Cecon E, Nureki O, Rivara S, Jockers R. Melatonin receptor structure and signaling. J Pineal Res 2024; 76:e12952. [PMID: 38587234 DOI: 10.1111/jpi.12952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 02/05/2024] [Accepted: 03/24/2024] [Indexed: 04/09/2024]
Abstract
Melatonin (5-methoxy-N-acetyltryptamine) binds with high affinity and specificity to membrane receptors. Several receptor subtypes exist in different species, of which the mammalian MT1 and MT2 receptors are the best-characterized. They are members of the G protein-coupled receptor superfamily, preferentially coupling to Gi/o proteins but also to other G proteins in a cell-context-depending manner. In this review, experts on melatonin receptors will summarize the current state of the field. We briefly report on the discovery and classification of melatonin receptors, then focus on the molecular structure of human MT1 and MT2 receptors and highlight the importance of molecular simulations to identify new ligands and to understand the structural dynamics of these receptors. We then describe the state-of-the-art of the intracellular signaling pathways activated by melatonin receptors and their complexes. Brief statements on the molecular toolbox available for melatonin receptor studies and future perspectives will round-up this review.
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Affiliation(s)
- Hiroyuki H Okamoto
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Erika Cecon
- Université Paris Cité, Institut Cochin, INSERM, CNRS, Paris, France
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Silvia Rivara
- Department of Food and Drug, University of Parma, Parma, Italy
| | - Ralf Jockers
- Université Paris Cité, Institut Cochin, INSERM, CNRS, Paris, France
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Scardino V, Di Filippo JI, Cavasotto CN. How good are AlphaFold models for docking-based virtual screening? iScience 2023; 26:105920. [PMID: 36686396 PMCID: PMC9852548 DOI: 10.1016/j.isci.2022.105920] [Citation(s) in RCA: 43] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 11/12/2022] [Accepted: 12/28/2022] [Indexed: 12/31/2022] Open
Abstract
A crucial component in structure-based drug discovery is the availability of high-quality three-dimensional structures of the protein target. Whenever experimental structures were not available, homology modeling has been, so far, the method of choice. Recently, AlphaFold (AF), an artificial-intelligence-based protein structure prediction method, has shown impressive results in terms of model accuracy. This outstanding success prompted us to evaluate how accurate AF models are from the perspective of docking-based drug discovery. We compared the high-throughput docking (HTD) performance of AF models with their corresponding experimental PDB structures using a benchmark set of 22 targets. The AF models showed consistently worse performance using four docking programs and two consensus techniques. Although AlphaFold shows a remarkable ability to predict protein architecture, this might not be enough to guarantee that AF models can be reliably used for HTD, and post-modeling refinement strategies might be key to increase the chances of success.
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Affiliation(s)
- Valeria Scardino
- Meton AI, Inc, Wilmington, DE 19801, USA
- Austral Institute for Applied Artificial Intelligence, Universidad Austral, Pilar, Buenos Aires, Argentina
| | - Juan I. Di Filippo
- Austral Institute for Applied Artificial Intelligence, Universidad Austral, Pilar, Buenos Aires, Argentina
- Computational Drug Design and Biomedical Informatics Laboratory, Instituto de Investigaciones en Medicina Traslacional (IIMT), Universidad Austral-CONICET, Pilar, Buenos Aires, Argentina
| | - Claudio N. Cavasotto
- Austral Institute for Applied Artificial Intelligence, Universidad Austral, Pilar, Buenos Aires, Argentina
- Computational Drug Design and Biomedical Informatics Laboratory, Instituto de Investigaciones en Medicina Traslacional (IIMT), Universidad Austral-CONICET, Pilar, Buenos Aires, Argentina
- Facultad de Ciencias Biomédicas, and Facultad de Ingeniería, Universidad Austral, Pilar, Buenos Aires, Argentina
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Elisi GM, Scalvini L, Lodola A, Bedini A, Spadoni G, Rivara S. In silico drug discovery of melatonin receptor ligands with therapeutic potential. Expert Opin Drug Discov 2022; 17:343-354. [PMID: 35255751 DOI: 10.1080/17460441.2022.2043846] [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: 11/04/2022]
Abstract
INTRODUCTION The neurohormone melatonin (N-acetyl-5-methoxytryptamine) regulates circadian rhythms exerting a variety of effects in the central nervous system and in periphery. These activities are mainly mediated by activation of MT1 and MT2 GPCRs. MT1/MT2 agonist compounds are used clinically for insomnia, depression, and circadian rhythm disturbances. AREA COVERED The following review describes the design strategies that have led to the identification of melatonin receptor ligands, guided by in silico approaches and molecular modeling. Initial ligand-based design, mainly relying on pharmacophore modeling and 3D-QSAR, has been flanked by structure-based virtual screening, given the recent availability of MT1 and MT2 crystal structures. Receptor ligands with different activity profiles, agonist/antagonist and subtype-selective compounds, are available. EXPERT OPINION An insight on the pharmacological characterization and therapeutic perspectives for relevant ligands is provided. In silico drug discovery has been instrumental in the design of novel ligands targeting melatonin receptors. Ligand-based approaches has led to the construction of a solid framework defining structure-activity relationships to obtain compounds with a tailored pharmacological profile. Structure-based techniques could integrate previous knowledge and provide compounds with novel chemotypes and pharmacological activity as drug candidates for disease conditions in which melatonin receptor ligands are currently being investigated, including cancer and pain.
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Affiliation(s)
- Gian Marco Elisi
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parma, Italy
| | - Laura Scalvini
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parma, Italy
| | - Alessio Lodola
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parma, Italy
| | - Annalida Bedini
- Dipartimento di Scienze Biomolecolari, Università degli Studi di Urbino "Carlo Bo", Urbino, Italy
| | - Gilberto Spadoni
- Dipartimento di Scienze Biomolecolari, Università degli Studi di Urbino "Carlo Bo", Urbino, Italy
| | - Silvia Rivara
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parma, Italy
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Structural Refinement of 2,4-Thiazolidinedione Derivatives as New Anticancer Agents Able to Modulate the BAG3 Protein. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27030665. [PMID: 35163936 PMCID: PMC8839660 DOI: 10.3390/molecules27030665] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/12/2022] [Accepted: 01/14/2022] [Indexed: 11/17/2022]
Abstract
The multidomain BAG3 protein is a member of the BAG (Bcl-2-associated athanogene) family of co-chaperones, involved in a wide range of protein-protein interactions crucial for many key cellular pathways, including autophagy, cytoskeletal dynamics, and apoptosis. Basal expression of BAG3 is elevated in several tumor cell lines, where it promotes cell survival signaling and apoptosis resistance through the interaction with many protein partners. In addition, its role as a key player of several hallmarks of cancer, such as metastasis, angiogenesis, autophagy activation, and apoptosis inhibition, has been established. Due to its involvement in malignant transformation, BAG3 has emerged as a potential and effective biological target to control multiple cancer-related signaling pathways. Recently, by using a multidisciplinary approach we reported the first synthetic BAG3 modulator interfering with its BAG domain (BD), based on a 2,4-thiazolidinedione scaffold and endowed with significant anti-proliferative activity. Here, a further in silico-driven selection of a 2,4-thiazolidinedione-based compound was performed. Thanks to a straightforward synthesis, relevant binding affinity for the BAG3BD domain, and attractive biological activities, this novel generation of compounds is of great interest for the development of further BAG3 binders, as well as for the elucidation of the biological roles of this protein in tumors. Specifically, we found compound 6 as a new BAG3 modulator with a relevant antiproliferative effect on two different cancer cell lines (IC50: A375 = 19.36 μM; HeLa = 18.67 μM).
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Bhunia SS, Saxena AK. Efficiency of Homology Modeling Assisted Molecular Docking in G-protein Coupled Receptors. Curr Top Med Chem 2021; 21:269-294. [PMID: 32901584 DOI: 10.2174/1568026620666200908165250] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 08/20/2020] [Accepted: 09/01/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Molecular docking is in regular practice to assess ligand affinity on a target protein crystal structure. In the absence of protein crystal structure, the homology modeling or comparative modeling is the best alternative to elucidate the relationship details between a ligand and protein at the molecular level. The development of accurate homology modeling (HM) and its integration with molecular docking (MD) is essential for successful, rational drug discovery. OBJECTIVE The G-protein coupled receptors (GPCRs) are attractive therapeutic targets due to their immense role in human pharmacology. The GPCRs are membrane-bound proteins with the complex constitution, and the understanding of their activation and inactivation mechanisms is quite challenging. Over the past decade, there has been a rapid expansion in the number of solved G-protein-coupled receptor (GPCR) crystal structures; however, the majority of the GPCR structures remain unsolved. In this context, HM guided MD has been widely used for structure-based drug design (SBDD) of GPCRs. METHODS The focus of this review is on the recent (i) developments on HM supported GPCR drug discovery in the absence of GPCR crystal structures and (ii) application of HM in understanding the ligand interactions at the binding site, virtual screening, determining receptor subtype selectivity and receptor behaviour in comparison with GPCR crystal structures. RESULTS The HM in GPCRs has been extremely challenging due to the scarcity in template structures. In such a scenario, it is difficult to get accurate HM that can facilitate understanding of the ligand-receptor interactions. This problem has been alleviated to some extent by developing refined HM based on incorporating active /inactive ligand information and inducing protein flexibility. In some cases, HM proteins were found to outscore crystal structures. CONCLUSION The developments in HM have been highly operative to gain insights about the ligand interaction at the binding site and receptor functioning at the molecular level. Thus, HM guided molecular docking may be useful for rational drug discovery for the GPCRs mediated diseases.
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Affiliation(s)
- Shome S Bhunia
- Global Institute of Pharmaceutical Education and Research, Kashipur, Uttarakhand, India
| | - Anil K Saxena
- Division of Medicinal and Process Chemistry, CSIR-CDRI, Lucknow 226031, India
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Kapla J, Rodríguez-Espigares I, Ballante F, Selent J, Carlsson J. Can molecular dynamics simulations improve the structural accuracy and virtual screening performance of GPCR models? PLoS Comput Biol 2021; 17:e1008936. [PMID: 33983933 PMCID: PMC8186765 DOI: 10.1371/journal.pcbi.1008936] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 06/08/2021] [Accepted: 04/02/2021] [Indexed: 01/14/2023] Open
Abstract
The determination of G protein-coupled receptor (GPCR) structures at atomic resolution has improved understanding of cellular signaling and will accelerate the development of new drug candidates. However, experimental structures still remain unavailable for a majority of the GPCR family. GPCR structures and their interactions with ligands can also be modelled computationally, but such predictions have limited accuracy. In this work, we explored if molecular dynamics (MD) simulations could be used to refine the accuracy of in silico models of receptor-ligand complexes that were submitted to a community-wide assessment of GPCR structure prediction (GPCR Dock). Two simulation protocols were used to refine 30 models of the D3 dopamine receptor (D3R) in complex with an antagonist. Close to 60 μs of simulation time was generated and the resulting MD refined models were compared to a D3R crystal structure. In the MD simulations, the receptor models generally drifted further away from the crystal structure conformation. However, MD refinement was able to improve the accuracy of the ligand binding mode. The best refinement protocol improved agreement with the experimentally observed ligand binding mode for a majority of the models. Receptor structures with improved virtual screening performance, which was assessed by molecular docking of ligands and decoys, could also be identified among the MD refined models. Application of weak restraints to the transmembrane helixes in the MD simulations further improved predictions of the ligand binding mode and second extracellular loop. These results provide guidelines for application of MD refinement in prediction of GPCR-ligand complexes and directions for further method development.
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Affiliation(s)
- Jon Kapla
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Ismael Rodríguez-Espigares
- Research Programme on Biomedical Informatics (GRIB), Department of Experimental and Health Sciences of Pompeu Fabra University (UPF), Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - Flavio Ballante
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Jana Selent
- Research Programme on Biomedical Informatics (GRIB), Department of Experimental and Health Sciences of Pompeu Fabra University (UPF), Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - Jens Carlsson
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
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Glatfelter GC, Jones AJ, Rajnarayanan RV, Dubocovich ML. Pharmacological Actions of Carbamate Insecticides at Mammalian Melatonin Receptors. J Pharmacol Exp Ther 2021; 376:306-321. [PMID: 33203660 PMCID: PMC7841424 DOI: 10.1124/jpet.120.000065] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 11/11/2020] [Indexed: 12/29/2022] Open
Abstract
Integrated in silico chemical clustering and melatonin receptor molecular modeling combined with in vitro 2-[125I]-iodomelatonin competition binding were used to identify carbamate insecticides with affinity for human melatonin receptor 1 (hMT1) and human melatonin receptor 2 (hMT2). Saturation and kinetic binding studies with 2-[125I]-iodomelatonin revealed lead carbamates (carbaryl, fenobucarb, bendiocarb, carbofuran) to be orthosteric ligands with antagonist apparent efficacy at hMT1 and agonist apparent efficacy at hMT2 Furthermore, using quantitative receptor autoradiography in coronal brain slices from C3H/HeN mice, carbaryl, fenobucarb, and bendiocarb competed for 2-[125I]-iodomelatonin binding in the suprachiasmatic nucleus (SCN), paraventricular nucleus of the thalamus (PVT), and pars tuberalis (PT) with affinities similar to those determined for the hMT1 receptor. Carbaryl (10 mg/kg i.p.) administered in vivo also competed ex vivo for 2-[125I]-iodomelatonin binding to the SCN, PVT, and PT, demonstrating the ability to reach brain melatonin receptors in C3H/HeN mice. Furthermore, the same dose of carbaryl given to C3H/HeN mice in constant dark for three consecutive days at subjective dusk (circadian time 10) phase-advanced circadian activity rhythms (mean = 0.91 hours) similar to melatonin (mean = 1.12 hours) when compared with vehicle (mean = 0.04 hours). Carbaryl-mediated phase shift of overt circadian activity rhythm onset is likely mediated via interactions with SCN melatonin receptors. Based on the pharmacological actions of carbaryl and other carbamate insecticides at melatonin receptors, exposure may modulate time-of-day information conveyed to the master biologic clock relevant to adverse health outcomes. SIGNIFICANCE STATEMENT: In silico chemical clustering and molecular modeling in conjunction with in vitro bioassays identified several carbamate insecticides (i.e., carbaryl, carbofuran, fenobucarb, bendiocarb) as pharmacologically active orthosteric melatonin receptor 1 and 2 ligands. This work further demonstrated that carbaryl competes for melatonin receptor binding in the master biological clock (suprachiasmatic nucleus) and phase-advances overt circadian activity rhythms in C3H/HeN mice, supporting the relevance of circadian effects when interpreting toxicological findings related to carbamate insecticide exposure.
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Affiliation(s)
- Grant C Glatfelter
- Department of Pharmacology and Toxicology (G.C.G., A.J.J., R.V.R., M.L.D.), Interdepartmental Neuroscience Program (A.J.J., M.L.D.), Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York
| | - Anthony J Jones
- Department of Pharmacology and Toxicology (G.C.G., A.J.J., R.V.R., M.L.D.), Interdepartmental Neuroscience Program (A.J.J., M.L.D.), Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York
| | - Rajendram V Rajnarayanan
- Department of Pharmacology and Toxicology (G.C.G., A.J.J., R.V.R., M.L.D.), Interdepartmental Neuroscience Program (A.J.J., M.L.D.), Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York
| | - Margarita L Dubocovich
- Department of Pharmacology and Toxicology (G.C.G., A.J.J., R.V.R., M.L.D.), Interdepartmental Neuroscience Program (A.J.J., M.L.D.), Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York
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Fells JI, Ai X, Weinglass A, Feng W, Lei Y, Finley M, Hoveyda HR, Fraser GL, Machacek M. Identification of free fatty acid receptor 2 agonists using virtual screening. Bioorg Med Chem Lett 2020; 30:127460. [DOI: 10.1016/j.bmcl.2020.127460] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 07/24/2020] [Accepted: 07/31/2020] [Indexed: 12/19/2022]
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9
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Caulfield TR, Hayes KE, Qiu Y, Coban M, Seok Oh J, Lane AL, Yoshimitsu T, Hazlehurst L, Copland JA, Tun HW. A Virtual Screening Platform Identifies Chloroethylagelastatin A as a Potential Ribosomal Inhibitor. Biomolecules 2020; 10:E1407. [PMID: 33027969 PMCID: PMC7599554 DOI: 10.3390/biom10101407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 09/11/2020] [Accepted: 09/29/2020] [Indexed: 12/03/2022] Open
Abstract
Chloroethylagelastatin A (CEAA) is an analogue of agelastatin A (AA), a natural alkaloid derived from a marine sponge. It is under development for therapeutic use against brain tumors as it has excellent central nervous system (CNS) penetration and pre-clinical therapeutic activity against brain tumors. Recently, AA was shown to inhibit protein synthesis by binding to the ribosomal A-site. In this study, we developed a novel virtual screening platform to perform a comprehensive screening of various AA analogues showing that AA analogues with proven therapeutic activity including CEAA have significant ribosomal binding capacity whereas therapeutically inactive analogues show poor ribosomal binding and revealing structural fingerprint features essential for drug-ribosome interactions. In particular, CEAA was found to have greater ribosomal binding capacity than AA. Biological tests showed that CEAA binds the ribosome and contributes to protein synthesis inhibition. Our findings suggest that CEAA may possess ribosomal inhibitor activity and that our virtual screening platform may be a useful tool in discovery and development of novel ribosomal inhibitors.
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Affiliation(s)
- Thomas R. Caulfield
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL 32224, USA; (Y.Q.); (M.C.); (A.L.L.); (J.A.C.)
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
- Department of Neurosurgery, Mayo Clinic, Jacksonville, FL 32224, USA
- Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Karen E. Hayes
- Modulation Therapeutics, Inc., Morgantown, WV 26506, USA;
| | - Yushi Qiu
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL 32224, USA; (Y.Q.); (M.C.); (A.L.L.); (J.A.C.)
| | - Mathew Coban
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL 32224, USA; (Y.Q.); (M.C.); (A.L.L.); (J.A.C.)
| | - Joon Seok Oh
- Department of Chemistry, University of North Florida, Jacksonville, FL 32224, USA;
| | - Amy L. Lane
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL 32224, USA; (Y.Q.); (M.C.); (A.L.L.); (J.A.C.)
- Department of Chemistry, University of North Florida, Jacksonville, FL 32224, USA;
| | - Takehiko Yoshimitsu
- Division of Pharmaceutical Sciences, Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University, 1-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530, Japan;
| | - Lori Hazlehurst
- Department of Pharmaceutical Sciences, West Virginia University, Morgantown, WV 26506, USA;
| | - John A. Copland
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL 32224, USA; (Y.Q.); (M.C.); (A.L.L.); (J.A.C.)
| | - Han W. Tun
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL 32224, USA; (Y.Q.); (M.C.); (A.L.L.); (J.A.C.)
- Department of Hematology/Oncology, Mayo Clinic, Jacksonville, FL 32224, USA
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Melatonin pharmacophoric motifs in the anancomeric spiranic oxindole-cycloalkane scaffold: Theoretical and 1H NMR conformational analysis. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2019.127267] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Ciani E, Fontaine R, Maugars G, Mizrahi N, Mayer I, Levavi-Sivan B, Weltzien FA. Melatonin receptors in Atlantic salmon stimulate cAMP levels in heterologous cell lines and show season-dependent daily variations in pituitary expression levels. J Pineal Res 2019; 67:e12590. [PMID: 31169933 DOI: 10.1111/jpi.12590] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 05/07/2019] [Accepted: 05/26/2019] [Indexed: 01/13/2023]
Abstract
The hormone melatonin connects environmental cues, such as photoperiod and temperature, with a number of physiological and behavioural processes, including seasonal reproduction, through binding to their cognate receptors. This study reports the structural, functional and physiological characterization of five high-affinity melatonin receptors (Mtnr1aaα, Mtnr1aaβ, Mtnr1ab, Mtnr1al, Mtnr1b) in Atlantic salmon. Phylogenetic analysis clustered salmon melatonin receptors into three monophyletic groups, Mtnr1A, Mtnr1Al and Mtnr1B, but no functional representative of the Mtnr1C group. Contrary to previous studies in vertebrates, pharmacological characterization of four receptors in COS-7, CHO and SH-SY5Y cell lines (Mtnr1Aaα, Mtnr1Aaβ, Mtnr1Ab, Mtnr1B) showed induction of intracellular cAMP levels following 2-iodomelatonin or melatonin exposure. No consistent response was measured after N-acetyl-serotonin or serotonin exposure. Melatonin receptor genes were expressed at all levels of the hypothalamo-pituitary-gonad axis, with three genes (mtnr1aaβ, mtnr1ab and mtnr1b) detected in the pituitary. Pituitary receptors displayed daily fluctuations in mRNA levels during spring, prior to the onset of gonadal maturation, but not in autumn, strongly implying a direct involvement of melatonin in seasonal processes regulated by the pituitary. To the best of our knowledge, this is the first report of cAMP induction mediated via melatonin receptors in a teleost species.
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Affiliation(s)
- Elia Ciani
- Department of Basic Sciences and Aquatic Medicine, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway
| | - Romain Fontaine
- Department of Basic Sciences and Aquatic Medicine, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway
| | - Gersende Maugars
- Department of Basic Sciences and Aquatic Medicine, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway
| | - Naama Mizrahi
- Department of Animal Sciences, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Ian Mayer
- Department of Production Animal Clinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway
| | - Berta Levavi-Sivan
- Department of Animal Sciences, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Finn-Arne Weltzien
- Department of Basic Sciences and Aquatic Medicine, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway
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Kang N, Wang XL, Zhao Y. Discovery of small molecule agonists targeting neuropeptide Y4 receptor using homology modeling and virtual screening. Chem Biol Drug Des 2019; 94:2064-2072. [PMID: 31444845 DOI: 10.1111/cbdd.13611] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 08/09/2019] [Accepted: 08/15/2019] [Indexed: 11/27/2022]
Abstract
Neuropeptide Y4 receptor has the most significant effect on body weight and fat mass in its physiological functions, and the activation of Y4 receptor has explicit role on losing weight. The Y4 receptor has been successfully applied in the development of anti-obesity agent, thus representing a potential therapeutic target for obesity treatment. Here, we reported the first discovery of small molecule agonists targeting Y4 receptor: three Y4 receptor models with active and inactive conformations were built, each model was submitted following structure-based virtual screening, and finally six hits were identified as Y4 receptor agonists. These results confirm the reliability of the constructed Y4 receptor models and the proposed computational strategy for investigating novel Y4 receptor agonists. These new small molecule Y4 receptor agonists will contribute to the further development of Y4 agonists as potential therapeutics and functional probes.
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Affiliation(s)
- Ning Kang
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Xiao-Lei Wang
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yaxue Zhao
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
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13
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Chen SY, Geng CA, Ma YB, Huang XY, Yang XT, Su LH, He XF, Li TZ, Deng ZT, Gao Z, Zhang XM, Chen JJ. Polybenzyls from Gastrodia elata, their agonistic effects on melatonin receptors and structure-activity relationships. Bioorg Med Chem 2019; 27:3299-3306. [PMID: 31204226 DOI: 10.1016/j.bmc.2019.06.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 05/30/2019] [Accepted: 06/05/2019] [Indexed: 10/26/2022]
Abstract
Gastrodia elata is a famous traditional Chinese herb with medicinal and edible application. In this study, nine polybenzyls (1-9), including six new ones (2-5, 7 and 9), were isolated from the EtOAc extract of G. elata. Five compounds 1, 3, 4, 6 and 8 were found to activate melatonin receptors. Especially, compound 1 showed agonistic effects on MT1 and MT2 receptors with EC50 values of 237 and 244 μM. For better understanding their structure-activity relationships (SARs), ten polybenzyl analogs were further synthesized and assayed for their activities on melatonin receptors. Preliminary SARs study suggested that two para-hydroxy groups were the key pharmacophore for maintaining activity. Molecular docking simulations verified that compound 1 could strongly interact with MT2 receptor by bonding to Phe 118, Gly 121, His 208, Try 294 and Ala 297 residues.
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Affiliation(s)
- Si-Yue Chen
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming 650201, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chang-An Geng
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming 650201, China
| | - Yun-Bao Ma
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming 650201, China
| | - Xiao-Yan Huang
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming 650201, China
| | - Xiao-Tong Yang
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming 650201, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Li-Hua Su
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming 650201, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiao-Feng He
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming 650201, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tian-Ze Li
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming 650201, China
| | - Zhen-Tao Deng
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming 650201, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhen Gao
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming 650201, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xue-Mei Zhang
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming 650201, China
| | - Ji-Jun Chen
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming 650201, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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14
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Lauro G, Cantone V, Potenza M, Fischer K, Koeberle A, Werz O, Riccio R, Bifulco G. Discovery of 3-hydroxy-3-pyrrolin-2-one-based mPGES-1 inhibitors using a multi-step virtual screening protocol. MEDCHEMCOMM 2018; 9:2028-2036. [PMID: 30746063 DOI: 10.1039/c8md00497h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 11/17/2018] [Indexed: 12/20/2022]
Abstract
Targeting microsomal prostaglandin E2 synthase-1 (mPGES-1) represents an efficient strategy for the development of novel drugs against inflammation and cancer with potentially reduced side effects. With this aim, a virtual screening was performed on a large library of commercially available molecules using the X-ray structure of mPGES-1 co-complexed with a potent inhibitor. Combining fast ligand-based shape alignment, molecular docking experiments, and qualitative analysis of the binding poses, a small set of molecules was selected for the subsequent steps of validation of the biological activity. Compounds 2 and 3, bearing the 3-hydroxy-3-pyrrolin-2-one nucleus, showed mPGES-1-inhibitory activity in the low micromolar range. These data highlighted the applicability of the reported virtual screening protocol for the selection of new mPGES-1 inhibitors as promising anti-inflammatory/anti-cancer drugs.
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Affiliation(s)
- Gianluigi Lauro
- Department of Pharmacy , University of Salerno , via Giovanni Paolo II 132 , 84084 Fisciano , Italy . ; ; Tel: +39 (0)89 969741
| | - Vincenza Cantone
- Department of Pharmacy , University of Salerno , via Giovanni Paolo II 132 , 84084 Fisciano , Italy . ; ; Tel: +39 (0)89 969741
| | - Marianna Potenza
- Department of Pharmacy , University of Salerno , via Giovanni Paolo II 132 , 84084 Fisciano , Italy . ; ; Tel: +39 (0)89 969741
| | - Katrin Fischer
- Department of Pharmaceutical/Medicinal Chemistry , Institute of Pharmacy , Friedrich-Schiller-University Jena , Philosophenweg 14 , D-07743 Jena , Germany
| | - Andreas Koeberle
- Department of Pharmaceutical/Medicinal Chemistry , Institute of Pharmacy , Friedrich-Schiller-University Jena , Philosophenweg 14 , D-07743 Jena , Germany
| | - Oliver Werz
- Department of Pharmaceutical/Medicinal Chemistry , Institute of Pharmacy , Friedrich-Schiller-University Jena , Philosophenweg 14 , D-07743 Jena , Germany
| | - Raffaele Riccio
- Department of Pharmacy , University of Salerno , via Giovanni Paolo II 132 , 84084 Fisciano , Italy . ; ; Tel: +39 (0)89 969741
| | - Giuseppe Bifulco
- Department of Pharmacy , University of Salerno , via Giovanni Paolo II 132 , 84084 Fisciano , Italy . ; ; Tel: +39 (0)89 969741
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15
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Alkozi HA, Sánchez Montero JM, Doadrio AL, Pintor J. Docking studies for melatonin receptors. Expert Opin Drug Discov 2017; 13:241-248. [PMID: 29271261 DOI: 10.1080/17460441.2018.1419184] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
INTRODUCTION Melatonin is a neurohormone that controls many relevant physiological processes beyond the control of circadian rhythms. Melatonin's actions are carried out by two main types of melatonin receptors; MT1 and MT2. These receptors are important, and not just because of the biological actions of its natural agonist; but also, because melatonin analogues can improve or antagonize their biological effect. Area covered: The following article describes the importance of melatonin as a biologically relevant molecule. It also defines the receptors for this substance, as well as the second messengers coupled to these receptors. Lastly, the article describes the amino acid residues involved in the docking process in both MT1 and MT2 melatonin receptors. Expert opinion: The biological actions of melatonin and their interpretations are becoming more relevant and therefore require the development of new pharmacological tools. Understanding the second messenger mechanisms involved in melatonin actions, as well as the characteristics of the docking of this molecule to MT1 and MT2 melatonin receptors, will permit the development of more selective agonists and antagonists which will help us to better understand this molecule as well to develop new therapeutic compounds.
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Affiliation(s)
- Hanan Awad Alkozi
- a Department of Biochemistry and Molecular Biology IV, Faculty of Optometry , Universidad Complutense de Madrid , Madrid , Spain
| | - José Maria Sánchez Montero
- b Department of Organic Chemistry and Pharmaceutical, Faculty of Pharmacy , Ciudad Universitaria , Madrid , Spain
| | - Antonio Luis Doadrio
- c Department of Inorganic Chemistry and Bioorganic, Faculty of Pharmacy , University Complutense of Madrid , Ciudad Universitaria, Madrid , Spain
| | - Jesus Pintor
- a Department of Biochemistry and Molecular Biology IV, Faculty of Optometry , Universidad Complutense de Madrid , Madrid , Spain
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16
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Mendoza-Figueroa H, Martínez-Gudiño G, Villanueva-Luna JE, Trujillo-Serrato JJ, Morales-Ríos MS. Pharmacophore modeling and conformational analysis in the gas phase and in aqueous solution of regioisomeric melatonin analogs. A theoretical and experimental study. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2016.12.040] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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17
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Popovska-Gorevski M, Dubocovich ML, Rajnarayanan RV. Carbamate Insecticides Target Human Melatonin Receptors. Chem Res Toxicol 2017; 30:574-582. [PMID: 28027439 DOI: 10.1021/acs.chemrestox.6b00301] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Carbaryl (1-naphthyl methylcarbamate) and carbofuran (2,3-dihydro-2,2-dimethyl-7-benzofuranyl methylcarbamate) are among the most toxic insecticides, implicated in a variety of diseases including diabetes and cancer among others. Using an integrated pharmacoinformatics based screening approach, we have identified these insecticides to be structural mimics of the neurohormone melatonin and were able to bind to the putative melatonin binding sites in MT1 and MT2 melatonin receptors in silico. Carbaryl and carbofuran then were tested for competition with 2-[125I]-iodomelatonin (300 pM) binding to hMT1 or hMT2 receptors stably expressed in CHO cells. Carbaryl and carbofuran showed higher affinity for competition with 2-[125I]-iodomelatonin binding to the hMT2 compared to the hMT1 melatonin receptor (33 and 35-fold difference, respectively) as predicted by the molecular modeling. In the presence of GTP (100 μM), which decouples the G-protein linked receptors to modulate signaling, the apparent efficacy of carbaryl and carbofuran for 2-[125I]-iodomelatonin binding for the hMT1 melatonin receptor was not affected but significantly decreased for the hMT2 melatonin receptor compatible with receptor antagonist/inverse agonist and agonist efficacy, respectively. Altogether, our data points to a potentially new mechanism through which carbamate insecticides carbaryl and carbofuran could impact human health by altering the homeostatic balance of key regulatory processes by directly binding to melatonin receptors.
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Affiliation(s)
- Marina Popovska-Gorevski
- Department of Pharmacology and Toxicology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo , Buffalo, New York 14221, United States
| | - Margarita L Dubocovich
- Department of Pharmacology and Toxicology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo , Buffalo, New York 14221, United States
| | - Rajendram V Rajnarayanan
- Department of Pharmacology and Toxicology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo , Buffalo, New York 14221, United States
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18
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Jockers R, Delagrange P, Dubocovich ML, Markus RP, Renault N, Tosini G, Cecon E, Zlotos DP. Update on melatonin receptors: IUPHAR Review 20. Br J Pharmacol 2016; 173:2702-25. [PMID: 27314810 DOI: 10.1111/bph.13536] [Citation(s) in RCA: 272] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 05/15/2016] [Accepted: 05/19/2016] [Indexed: 02/06/2023] Open
Abstract
Melatonin receptors are seven transmembrane-spanning proteins belonging to the GPCR superfamily. In mammals, two melatonin receptor subtypes exist - MT1 and MT2 - encoded by the MTNR1A and MTNR1B genes respectively. The current review provides an update on melatonin receptors by the corresponding subcommittee of the International Union of Basic and Clinical Pharmacology. We will highlight recent developments of melatonin receptor ligands, including radioligands, and give an update on the latest phenotyping results of melatonin receptor knockout mice. The current status and perspectives of the structure of melatonin receptor will be summarized. The physiological importance of melatonin receptor dimers and biologically important and type 2 diabetes-associated genetic variants of melatonin receptors will be discussed. The role of melatonin receptors in physiology and disease will be further exemplified by their functions in the immune system and the CNS. Finally, antioxidant and free radical scavenger properties of melatonin and its relation to melatonin receptors will be critically addressed.
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Affiliation(s)
- Ralf Jockers
- Inserm, U1016, Institut Cochin, Paris, France.,CNRS UMR 8104, Paris, France.,University Paris Descartes, Paris, France
| | | | - Margarita L Dubocovich
- Department Pharmacology and Toxicology, Jacobs School of Medicine and Biomedical Science, University at Buffalo (SUNY), Buffalo, USA
| | - Regina P Markus
- Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | | | - Gianluca Tosini
- Neuroscience Institute and Department of Pharmacology and Toxicology, Morehouse School of Medicine, Atlanta, GA, USA
| | - Erika Cecon
- Inserm, U1016, Institut Cochin, Paris, France.,CNRS UMR 8104, Paris, France.,University Paris Descartes, Paris, France
| | - Darius P Zlotos
- Department of Pharmaceutical Chemistry, The German University in Cairo, New Cairo City, Cairo, Egypt
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19
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Thomas T, Chalmers DK, Yuriev E. Homology Modeling and Docking Evaluation of Human Muscarinic Acetylcholine Receptors. NEUROMETHODS 2016. [DOI: 10.1007/978-1-4939-2858-3_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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20
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Spyrakis F, Cavasotto CN. Open challenges in structure-based virtual screening: Receptor modeling, target flexibility consideration and active site water molecules description. Arch Biochem Biophys 2015; 583:105-19. [DOI: 10.1016/j.abb.2015.08.002] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 08/03/2015] [Accepted: 08/03/2015] [Indexed: 01/05/2023]
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21
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Callegari D, Pala D, Scalvini L, Tognolini M, Incerti M, Rivara S, Mor M, Lodola A. Comparative Analysis of Virtual Screening Approaches in the Search for Novel EphA2 Receptor Antagonists. Molecules 2015; 20:17132-51. [PMID: 26393553 PMCID: PMC6331951 DOI: 10.3390/molecules200917132] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 09/08/2015] [Accepted: 09/11/2015] [Indexed: 11/29/2022] Open
Abstract
The EphA2 receptor and its ephrin-A1 ligand form a key cell communication system, which has been found overexpressed in many cancer types and involved in tumor growth. Recent medicinal chemistry efforts have identified bile acid derivatives as low micromolar binders of the EphA2 receptor. However, these compounds suffer from poor physicochemical properties, hampering their use in vivo. The identification of compounds able to disrupt the EphA2-ephrin-A1 complex lacking the bile acid scaffold may lead to new pharmacological tools suitable for in vivo studies. To identify the most promising virtual screening (VS) protocol aimed at finding novel EphA2 antagonists, we investigated the ability of both ligand-based and structure-based approaches to retrieve known EphA2 antagonists from libraries of decoys with similar molecular properties. While ligand-based VSs were conducted using UniPR129 and ephrin-A1 ligand as reference structures, structure-based VSs were performed with Glide, using the X-ray structure of the EphA2 receptor/ephrin-A1 complex. A comparison of enrichment factors showed that ligand-based approaches outperformed the structure-based ones, suggesting ligand-based methods using the G-H loop of ephrin-A1 ligand as template as the most promising protocols to search for novel EphA2 antagonists.
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Affiliation(s)
- Donatella Callegari
- Dipartimento di Farmacia, Università degli Studi di Parma, Parma 43124, Italy.
| | - Daniele Pala
- Dipartimento di Farmacia, Università degli Studi di Parma, Parma 43124, Italy.
| | - Laura Scalvini
- Dipartimento di Farmacia, Università degli Studi di Parma, Parma 43124, Italy.
| | | | - Matteo Incerti
- Dipartimento di Farmacia, Università degli Studi di Parma, Parma 43124, Italy.
| | - Silvia Rivara
- Dipartimento di Farmacia, Università degli Studi di Parma, Parma 43124, Italy.
| | - Marco Mor
- Dipartimento di Farmacia, Università degli Studi di Parma, Parma 43124, Italy.
| | - Alessio Lodola
- Dipartimento di Farmacia, Università degli Studi di Parma, Parma 43124, Italy.
- Department of Applied Sciences, Northumbria University at Newcastle, Newcastle-Upon-Tyne, NE1 8ST, UK.
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22
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de la Fuente Revenga M, Fernández-Sáez N, Herrera-Arozamena C, Morales-García JA, Alonso-Gil S, Pérez-Castillo A, Caignard DH, Rivara S, Rodríguez-Franco MI. Novel N-Acetyl Bioisosteres of Melatonin: Melatonergic Receptor Pharmacology, Physicochemical Studies, and Phenotypic Assessment of Their Neurogenic Potential. J Med Chem 2015; 58:4998-5014. [PMID: 26023814 DOI: 10.1021/acs.jmedchem.5b00245] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Herein we present a new family of melatonin-based compounds, in which the acetamido group of melatonin has been bioisosterically replaced by a series of reversed amides and azoles, such as oxazole, 1,2,4-oxadiazole, and 1,3,4-oxadiazole, as well as other related five-membered heterocycles, namely, 1,3,4-oxadiazol(thio)ones, 1,3,4-triazol(thio)ones, and an 1,3,4-thiadiazole. New compounds were fully characterized at melatonin receptors (MT1R and MT2R), and results were rationalized by superimposition studies of their structures to the bioactive conformation of melatonin. We also found that several of these melatonin-based compounds promoted differentiation of rat neural stem cells to a neuronal phenotype in vitro, in some cases to a higher extent than melatonin. This unique profile constitutes the starting point for further pharmacological studies to assess the mechanistic pathways and the relevance of neurogenesis induced by melatonin-related structures.
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Affiliation(s)
- Mario de la Fuente Revenga
- †Instituto de Química Médica, Consejo Superior de Investigaciones Científicas (IQM-CSIC), C/Juan de la Cierva 3, 28006 Madrid, Spain
| | - Nerea Fernández-Sáez
- †Instituto de Química Médica, Consejo Superior de Investigaciones Científicas (IQM-CSIC), C/Juan de la Cierva 3, 28006 Madrid, Spain
| | - Clara Herrera-Arozamena
- †Instituto de Química Médica, Consejo Superior de Investigaciones Científicas (IQM-CSIC), C/Juan de la Cierva 3, 28006 Madrid, Spain
| | - José A Morales-García
- ‡Instituto de Investigaciones Biomédicas "Alberto Sols", Consejo Superior de Investigaciones Científicas (IIB-CSIC), C/Arturo Duperier 4, 28029 Madrid, Spain.,§Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), C/Valderrebollo 5, 28031 Madrid, Spain
| | - Sandra Alonso-Gil
- ‡Instituto de Investigaciones Biomédicas "Alberto Sols", Consejo Superior de Investigaciones Científicas (IIB-CSIC), C/Arturo Duperier 4, 28029 Madrid, Spain.,§Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), C/Valderrebollo 5, 28031 Madrid, Spain
| | - Ana Pérez-Castillo
- ‡Instituto de Investigaciones Biomédicas "Alberto Sols", Consejo Superior de Investigaciones Científicas (IIB-CSIC), C/Arturo Duperier 4, 28029 Madrid, Spain.,§Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), C/Valderrebollo 5, 28031 Madrid, Spain
| | - Daniel-Henri Caignard
- ∥Institut de Recherches Servier, 125 Chemin de Ronde, 78290 Croissy sur Seine, France
| | - Silvia Rivara
- ⊥Dipartimento di Farmacia, Università degli Studi di Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | - María Isabel Rodríguez-Franco
- †Instituto de Química Médica, Consejo Superior de Investigaciones Científicas (IQM-CSIC), C/Juan de la Cierva 3, 28006 Madrid, Spain
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23
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Xu J, Yuan H, Ran T, Zhang Y, Liu H, Lu S, Xiong X, Xu A, Jiang Y, Lu T, Chen Y. A selectivity study of sodium-dependent glucose cotransporter 2/sodium-dependent glucose cotransporter 1 inhibitors by molecular modeling. J Mol Recognit 2015; 28:467-79. [DOI: 10.1002/jmr.2464] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 01/15/2015] [Accepted: 01/15/2015] [Indexed: 01/01/2023]
Affiliation(s)
- Jinxing Xu
- Laboratory of Molecular Design and Drug Discovery, School of Science; China Pharmaceutical University; 639 Longmian Avenue Nanjing 211198 China
| | - Haoliang Yuan
- Key Laboratory of Nuclear Medicine, Ministry of Health, Jiangsu Key Laboratory of Molecular Nuclear Medicine; Jiangsu Institute of Nuclear Medicine; Wuxi 214063 China
| | - Ting Ran
- Laboratory of Molecular Design and Drug Discovery, School of Science; China Pharmaceutical University; 639 Longmian Avenue Nanjing 211198 China
| | - Yanmin Zhang
- Laboratory of Molecular Design and Drug Discovery, School of Science; China Pharmaceutical University; 639 Longmian Avenue Nanjing 211198 China
| | - Haichun Liu
- Laboratory of Molecular Design and Drug Discovery, School of Science; China Pharmaceutical University; 639 Longmian Avenue Nanjing 211198 China
| | - Shuai Lu
- Laboratory of Molecular Design and Drug Discovery, School of Science; China Pharmaceutical University; 639 Longmian Avenue Nanjing 211198 China
| | - Xiao Xiong
- Laboratory of Molecular Design and Drug Discovery, School of Science; China Pharmaceutical University; 639 Longmian Avenue Nanjing 211198 China
| | - Anyang Xu
- Laboratory of Molecular Design and Drug Discovery, School of Science; China Pharmaceutical University; 639 Longmian Avenue Nanjing 211198 China
| | - Yulei Jiang
- Laboratory of Molecular Design and Drug Discovery, School of Science; China Pharmaceutical University; 639 Longmian Avenue Nanjing 211198 China
| | - Tao Lu
- Laboratory of Molecular Design and Drug Discovery, School of Science; China Pharmaceutical University; 639 Longmian Avenue Nanjing 211198 China
- State Key Laboratory of Natural Medicines, School of Science; China Pharmaceutical University; 639 Longmian Avenue Nanjing 211198 China
| | - Yadong Chen
- Laboratory of Molecular Design and Drug Discovery, School of Science; China Pharmaceutical University; 639 Longmian Avenue Nanjing 211198 China
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24
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Beuming T, Lenselink B, Pala D, McRobb F, Repasky M, Sherman W. Docking and Virtual Screening Strategies for GPCR Drug Discovery. Methods Mol Biol 2015; 1335:251-76. [PMID: 26260606 DOI: 10.1007/978-1-4939-2914-6_17] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Progress in structure determination of G protein-coupled receptors (GPCRs) has made it possible to apply structure-based drug design (SBDD) methods to this pharmaceutically important target class. The quality of GPCR structures available for SBDD projects fall on a spectrum ranging from high resolution crystal structures (<2 Å), where all water molecules in the binding pocket are resolved, to lower resolution (>3 Å) where some protein residues are not resolved, and finally to homology models that are built using distantly related templates. Each GPCR project involves a distinct set of opportunities and challenges, and requires different approaches to model the interaction between the receptor and the ligands. In this review we will discuss docking and virtual screening to GPCRs, and highlight several refinement and post-processing steps that can be used to improve the accuracy of these calculations. Several examples are discussed that illustrate specific steps that can be taken to improve upon the docking and virtual screening accuracy. While GPCRs are a unique target class, many of the methods and strategies outlined in this review are general and therefore applicable to other protein families.
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Affiliation(s)
- Thijs Beuming
- Schrödinger, Inc., 120 West 45th Street, New York, NY, 10036, USA,
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25
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Cavasotto CN, Palomba D. Expanding the horizons of G protein-coupled receptor structure-based ligand discovery and optimization using homology models. Chem Commun (Camb) 2015; 51:13576-94. [DOI: 10.1039/c5cc05050b] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
We show the key role of structural homology models in GPCR structure-based lead discovery and optimization, highlighting methodological aspects, recent progress and future directions.
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Affiliation(s)
- Claudio N. Cavasotto
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) - CONICET - Partner Institute of the Max Planck Society
- Buenos Aires
- Argentina
| | - Damián Palomba
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) - CONICET - Partner Institute of the Max Planck Society
- Buenos Aires
- Argentina
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26
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Kakarala KK, Jamil K, Devaraji V. Structure and putative signaling mechanism of Protease activated receptor 2 (PAR2) - a promising target for breast cancer. J Mol Graph Model 2014; 53:179-199. [PMID: 25173751 DOI: 10.1016/j.jmgm.2014.07.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 07/16/2014] [Accepted: 07/21/2014] [Indexed: 12/12/2022]
Abstract
Experimental evidences have observed enhanced expression of protease activated receptor 2 (PAR2) in breast cancer consistently. However, it is not yet recognized as an important therapeutic target for breast cancer as the primary molecular mechanisms of its activation are not yet well-defined. Nevertheless, recent reports on the mechanism of GPCR activation and signaling have given new insights to GPCR functioning. In the light of these details, we attempted to understand PAR2 structure & function using molecular modeling techniques. In this work, we generated averaged representative stable models of PAR2, using protease activated receptor 1 (PAR1) as a template and selected conformation based on their binding affinity with PAR2 specific agonist, GB110. Further, the selected model was used for studying the binding affinity of putative ligands. The selected ligands were based on a recent publication on phylogenetic analysis of Class A rhodopsin family of GPCRs. This study reports putative ligands, their interacting residues, binding affinity and molecular dynamics simulation studies on PAR2-ligand complexes. The results reported from this study would be useful for researchers and academicians to investigate PAR2 function as its physiological role is still hypothetical. Further, this information may provide a novel therapeutic scheme to manage breast cancer.
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Affiliation(s)
- Kavita Kumari Kakarala
- Centre for Biotechnology and Bioinformatics (CBB), School of Life Sciences, Jawaharlal Nehru Institute of Advanced Studies (JNIAS), 6th Floor, Buddha Bhawan, M.G. Road, Secunderabad 500003, Andhra Pradesh, India.
| | - Kaiser Jamil
- Centre for Biotechnology and Bioinformatics (CBB), School of Life Sciences, Jawaharlal Nehru Institute of Advanced Studies (JNIAS), 6th Floor, Buddha Bhawan, M.G. Road, Secunderabad 500003, Andhra Pradesh, India
| | - Vinod Devaraji
- College of Pharmacy, Madras Medical College, E.V.R. Periyar Salai, Chennai 600003, India
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27
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An exhaustive yet simple virtual screening campaign against Sortase A from multiple drug resistant Staphylococcus aureus. Mol Biol Rep 2014; 41:5167-75. [PMID: 24797540 DOI: 10.1007/s11033-014-3384-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Accepted: 04/22/2014] [Indexed: 10/25/2022]
Abstract
Methicillin resistant Staphylococcus aureus (MRSA) is one of the challenging bacterial pathogen due to its acquired resistance to the β lactam antibiotics. The Sortase A is an enzyme of Gram-positive bacteria including S. aureus to anchor surface proteins to the cell wall. Sortase A is well studied enzyme and considered as the drug target against MRSA. Sortase A plays active role in anchoring the virulence proteins on the cell wall of the Gram-positive bacteria. The inhibition of Sortase A activity results in the separation of S. aureus from the host cells and ultimately alleviation of the infection. Here, we adapted a structure-based virtual screening protocol which helped in identification of novel potential inhibitors of Sortase A. The protocol involved the docking of a chemical library of druglike compounds with the Sortase A binding site represented by multiple crystal structures. The compounds were ranked by multiple scoring functions and shortlisted for future experimental screening. The method resulted in shortlisting of three compounds as potential novel inhibitors of Sortase A out of a large chemical library. The high rankings of shortlisted compounds estimated by multiple scoring functions showed their binding potential with Sortase A. The results are proved to be a simple yet efficient choice of structure-based virtual screening. The identified compounds are druglike and show high rankings among all set protocols of the virtual screening. We hope that the study would eventually help to expedite the discovery of novel drug candidates against MRSA.
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Thomas T, McLean KC, McRobb FM, Manallack DT, Chalmers DK, Yuriev E. Homology modeling of human muscarinic acetylcholine receptors. J Chem Inf Model 2013; 54:243-53. [PMID: 24328076 DOI: 10.1021/ci400502u] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We have developed homology models of the acetylcholine muscarinic receptors M₁R-M₅R, based on the β₂-adrenergic receptor crystal as the template. This is the first report of homology modeling of all five subtypes of acetylcholine muscarinic receptors with binding sites optimized for ligand binding. The models were evaluated for their ability to discriminate between muscarinic antagonists and decoy compounds using virtual screening using enrichment factors, area under the ROC curve (AUC), and an early enrichment measure, LogAUC. The models produce rational binding modes of docked ligands as well as good enrichment capacity when tested against property-matched decoy libraries, which demonstrates their unbiased predictive ability. To test the relative effects of homology model template selection and the binding site optimization procedure, we generated and evaluated a naïve M₂R model, using the M₃R crystal structure as a template. Our results confirm previous findings that binding site optimization using ligand(s) active at a particular receptor, i.e. including functional knowledge into the model building process, has a more pronounced effect on model quality than target-template sequence similarity. The optimized M₁R-M₅R homology models are made available as part of the Supporting Information to allow researchers to use these structures, compare them to their own results, and thus advance the development of better modeling approaches.
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Affiliation(s)
- Trayder Thomas
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University (Parkville Campus) , 381 Royal Parade, Parkville, VIC 3052 Australia
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Zlotos DP, Jockers R, Cecon E, Rivara S, Witt-Enderby PA. MT1 and MT2 Melatonin Receptors: Ligands, Models, Oligomers, and Therapeutic Potential. J Med Chem 2013; 57:3161-85. [DOI: 10.1021/jm401343c] [Citation(s) in RCA: 114] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Darius. P. Zlotos
- Department
of Pharmaceutical Chemistry, The German University in Cairo, New Cairo City, 11835 Cairo, Egypt
| | - Ralf Jockers
- Inserm, U1016,
Institut Cochin, Paris, France
- CNRS UMR
8104, Paris, France
- Univ. Paris Descartes, Sorbonne Paris Cite, Paris, France
| | - Erika Cecon
- Department
of Physiology, Institute of Bioscience, University of Sao Paulo, Sao Paulo 05508-090, Brazil
| | - Silvia Rivara
- Dipartimento
di Farmacia, Università degli Studi di Parma, Parco Area
delle Scienze 27/A, 43124 Parma, Italy
| | - Paula A. Witt-Enderby
- Division
of Pharmaceutical Sciences, School of Pharmacy, Duquesne University, 421 Mellon Hall, Pittsburgh, Pennsylvania 15282, United States
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30
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Chan KH, Wong YH. A molecular and chemical perspective in defining melatonin receptor subtype selectivity. Int J Mol Sci 2013; 14:18385-406. [PMID: 24018885 PMCID: PMC3794785 DOI: 10.3390/ijms140918385] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2013] [Revised: 07/16/2013] [Accepted: 08/26/2013] [Indexed: 12/15/2022] Open
Abstract
Melatonin is primarily synthesized and secreted by the pineal gland during darkness in a normal diurnal cycle. In addition to its intrinsic antioxidant property, the neurohormone has renowned regulatory roles in the control of circadian rhythm and exerts its physiological actions primarily by interacting with the G protein-coupled MT1 and MT2 transmembrane receptors. The two melatonin receptor subtypes display identical ligand binding characteristics and mediate a myriad of signaling pathways, including adenylyl cyclase inhibition, phospholipase C stimulation and the regulation of other effector molecules. Both MT1 and MT2 receptors are widely expressed in the central nervous system as well as many peripheral tissues, but each receptor subtype can be linked to specific functional responses at the target tissue. Given the broad therapeutic implications of melatonin receptors in chronobiology, immunomodulation, endocrine regulation, reproductive functions and cancer development, drug discovery and development programs have been directed at identifying chemical molecules that bind to the two melatonin receptor subtypes. However, all of the melatoninergics in the market act on both subtypes of melatonin receptors without significant selectivity. To facilitate the design and development of novel therapeutic agents, it is necessary to understand the intrinsic differences between MT1 and MT2 that determine ligand binding, functional efficacy, and signaling specificity. This review summarizes our current knowledge in differentiating MT1 and MT2 receptors and their signaling capacities. The use of homology modeling in the mapping of the ligand-binding pocket will be described. Identification of conserved and distinct residues will be tremendously useful in the design of highly selective ligands.
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MESH Headings
- Animals
- Humans
- Melatonin/metabolism
- Receptor, Melatonin, MT1/chemistry
- Receptor, Melatonin, MT1/metabolism
- Receptor, Melatonin, MT2/chemistry
- Receptor, Melatonin, MT2/metabolism
- Receptors, Melatonin/chemistry
- Receptors, Melatonin/metabolism
- Signal Transduction
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Affiliation(s)
- King Hang Chan
- Biotechnology Research Institute, State Key Laboratory of Molecular Neuroscience, Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong.
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Sastry GM, Inakollu VSS, Sherman W. Boosting Virtual Screening Enrichments with Data Fusion: Coalescing Hits from Two-Dimensional Fingerprints, Shape, and Docking. J Chem Inf Model 2013; 53:1531-42. [DOI: 10.1021/ci300463g] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- G. Madhavi Sastry
- Schrödinger, Sanali Infopark, 8-2-120/113, Banjara Hills,
Hyderabad 500034, Andhra Pradesh, India
| | - V. S. Sandeep Inakollu
- Schrödinger, Sanali Infopark, 8-2-120/113, Banjara Hills,
Hyderabad 500034, Andhra Pradesh, India
| | - Woody Sherman
- Schrödinger, 120 West 45th Street, New York,
New York 10036, United States
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