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de Lima Menezes G, Sales Bezerra K, Nobre Oliveira JI, Fontenele Araújo J, Soares Galvão D, Alves da Silva R, Vogel Saivish M, Laino Fulco U. Quantum mechanics insights into melatonin and analogs binding to melatonin MT 1 and MT 2 receptors. Sci Rep 2024; 14:10922. [PMID: 38740789 DOI: 10.1038/s41598-024-59786-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 04/15/2024] [Indexed: 05/16/2024] Open
Abstract
Melatonin receptors MT1 and MT2 are G protein-coupled receptors that mediate the effects of melatonin, a hormone involved in circadian rhythms and other physiological functions. Understanding the molecular interactions between these receptors and their ligands is crucial for developing novel therapeutic agents. In this study, we used molecular docking, molecular dynamics simulations, and quantum mechanics calculation to investigate the binding modes and affinities of three ligands: melatonin (MLT), ramelteon (RMT), and 2-phenylmelatonin (2-PMT) with both receptors. Based on the results, we identified key amino acids that contributed to the receptor-ligand interactions, such as Gln181/194, Phe179/192, and Asn162/175, which are conserved in both receptors. Additionally, we described new meaningful interactions with Gly108/Gly121, Val111/Val124, and Val191/Val204. Our results provide insights into receptor-ligand recognition's structural and energetic determinants and suggest potential strategies for designing more optimized molecules. This study enhances our understanding of receptor-ligand interactions and offers implications for future drug development.
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Affiliation(s)
- Gabriela de Lima Menezes
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande no Norte, Natal, RN, 59072-970, Brazil
- Bioinformatics Multidisciplinary Environment, Programa de Pós Graduação em Bioinformática, Universidade Federal do Rio Grande do Norte, Natal, RN, 59078-400, Brazil
| | - Katyanna Sales Bezerra
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande no Norte, Natal, RN, 59072-970, Brazil
- Applied Physics Department, University of Campinas, Campinas, São Paulo, 13083-859, Brazil
| | - Jonas Ivan Nobre Oliveira
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande no Norte, Natal, RN, 59072-970, Brazil
| | - John Fontenele Araújo
- Departamento de Fisiologia e Comportamento, Universidade Federal do Rio Grande no Norte, Natal, RN, 59072-970, Brazil
| | - Douglas Soares Galvão
- Applied Physics Department, University of Campinas, Campinas, São Paulo, 13083-859, Brazil
| | - Roosevelt Alves da Silva
- Unidade Especial de Ciências Exatas, Universidade Federal de Jataí, Jataí, GO, 75801-615, Brazil
| | - Marielena Vogel Saivish
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José Do Rio Preto, São José Do Rio, Preto, SP, 15090-000, Brazil
- Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Brazilian Biosciences National Laboratory, Campinas, SP, 13083-100, Brazil
| | - Umberto Laino Fulco
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande no Norte, Natal, RN, 59072-970, Brazil.
- Bioinformatics Multidisciplinary Environment, Programa de Pós Graduação em Bioinformática, Universidade Federal do Rio Grande do Norte, Natal, RN, 59078-400, Brazil.
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Bedini A, Boutin JA, Legros C, Zlotos DP, Spadoni G. Industrial and academic approaches to the search for alternative melatonin receptor ligands: An historical survey. J Pineal Res 2024; 76:e12953. [PMID: 38682544 DOI: 10.1111/jpi.12953] [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: 10/07/2023] [Revised: 03/05/2024] [Accepted: 03/24/2024] [Indexed: 05/01/2024]
Abstract
The search for melatonin receptor agonists formed the main part of melatonin medicinal chemistry programs for the last three decades. In this short review, we summarize the two main aspects of these programs: the development of all the necessary tools to characterize the newly synthesized ligands at the two melatonin receptors MT1 and MT2, and the medicinal chemist's approaches to find chemically diverse ligands at these receptors. Both strategies are described. It turns out that the main source of tools were industrial laboratories, while the medicinal chemistry was mainly carried out in academia. Such complete accounts are interesting, as they delineate the spirits in which the teams were working demonstrating their strength and innovative character. Most of the programs were focused on nonselective agonists and few of them reached the market. In contrast, discovery of MT1-selective agonists and melatonergic antagonists with proven in vivo activity and MT1 or MT2-selectivity is still in its infancy, despite the considerable interest that subtype selective compounds may bring in the domain, as the physiological respective roles of the two subtypes of melatonin receptors, is still poorly understood. Poly-pharmacology applications and multitarget ligands have also been considered.
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MESH Headings
- Ligands
- Humans
- Animals
- Receptor, Melatonin, MT2/metabolism
- Receptor, Melatonin, MT2/agonists
- Receptor, Melatonin, MT1/metabolism
- Receptor, Melatonin, MT1/agonists
- Receptor, Melatonin, MT1/antagonists & inhibitors
- Receptors, Melatonin/metabolism
- Receptors, Melatonin/agonists
- Melatonin/metabolism
- History, 20th Century
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Affiliation(s)
- Annalida Bedini
- Dipartimento di Scienze Biomolecolari, Università degli Studi di Urbino Carlo Bo, Urbino, Italy
| | - Jean A Boutin
- Laboratory of Neuroendocrine Endocrine and Germinal Differentiation and Communication (NorDiC), Univ Rouen Normandie, Inserm, NorDiC, Rouen, France
| | | | - Darius P Zlotos
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, The German University in Cairo, New Cairo City, Egypt
| | - Gilberto Spadoni
- Dipartimento di Scienze Biomolecolari, Università degli Studi di Urbino Carlo Bo, Urbino, Italy
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3
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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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4
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Bedini A, Elisi GM, Fanini F, Retini M, Scalvini L, Pasquini S, Contri C, Varani K, Spadoni G, Mor M, Vincenzi F, Rivara S. Binding and unbinding of potent melatonin receptor ligands: Mechanistic simulations and experimental evidence. J Pineal Res 2024; 76:e12941. [PMID: 38606814 DOI: 10.1111/jpi.12941] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 01/04/2024] [Accepted: 01/10/2024] [Indexed: 04/13/2024]
Abstract
The labeled ligand commonly employed in competition binding studies for melatonin receptor ligands, 2-[125I]iodomelatonin, showed slow dissociation with different half-lives at the two receptor subtypes. This may affect the operational measures of affinity constants, which at short incubation times could not be obtained in equilibrium conditions, and structure-activity relationships, as the Ki values of tested ligands could depend on either interaction at the binding site or the dissociation path. To address these issues, the kinetic and saturation binding parameters of 2-[125I]iodomelatonin as well as the competition constants for a series of representative ligands were measured at a short (2 h) and a long (20 h) incubation time. Concurrently, we simulated by molecular modeling the dissociation path of 2-iodomelatonin from MT1 and MT2 receptors and investigated the role of interactions at the binding site on the stereoselectivity observed for the enantiomers of the subtype-selective ligand UCM1014. We found that equilibrium conditions for 2-[125I]iodomelatonin binding can be reached only with long incubation times, particularly for the MT2 receptor subtype, for which a time of 20 h approximates this condition. On the other hand, measured Ki values for a set of ligands including agonists, antagonists, nonselective, and subtype-selective compounds were not significantly affected by the length of incubation, suggesting that structure-activity relationships based on data collected at shorter time reflect different interactions at the binding site. Molecular modeling simulations evidenced that the slower dissociation of 2-iodomelatonin from the MT2 receptor can be related to the restricted mobility of a gatekeeper tyrosine along a lipophilic path from the binding site to the membrane bilayer. The enantiomers of the potent, MT2-selective agonist UCM1014 were separately synthesized and tested. Molecular dynamics simulations of the receptor-ligand complexes provided an explanation for their stereoselectivity as due to the preference shown by the eutomer at the binding site for the most abundant axial conformation adopted by the ligand in solution. These results suggest that, despite the slow-binding kinetics occurring for the labeled ligand, affinity measures at shorter incubation times give robust results consistent with known structure-activity relationships and with interactions taken at the receptor binding site.
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Affiliation(s)
- Annalida Bedini
- Dipartimento di Scienze Biomolecolari, Università degli Studi di Urbino Carlo Bo, Urbino, Italy
| | - Gian Marco Elisi
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parma, Italy
| | - Fabiola Fanini
- Dipartimento di Scienze Biomolecolari, Università degli Studi di Urbino Carlo Bo, Urbino, Italy
| | - Michele Retini
- Dipartimento di Scienze Biomolecolari, Università degli Studi di Urbino Carlo Bo, Urbino, Italy
| | - Laura Scalvini
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parma, Italy
| | - Silvia Pasquini
- Dipartimento di Scienze Chimiche, Farmaceutiche ed Agrarie, Università degli Studi di Ferrara, Ferrara, Italy
| | - Chiara Contri
- Dipartimento di Medicina Traslazionale, Università degli Studi di Ferrara, Ferrara, Italy
| | - Katia Varani
- Dipartimento di Medicina Traslazionale, Università degli Studi di Ferrara, Ferrara, Italy
| | - Gilberto Spadoni
- Dipartimento di Scienze Biomolecolari, Università degli Studi di Urbino Carlo Bo, Urbino, Italy
| | - Marco Mor
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parma, Italy
| | - Fabrizio Vincenzi
- Dipartimento di Medicina Traslazionale, Università degli Studi di Ferrara, Ferrara, Italy
| | - Silvia Rivara
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parma, Italy
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Albasri OWA, Kumar PV, Rajagopal MS. Development of Computational In Silico Model for Nano Lipid Carrier Formulation of Curcumin. Molecules 2023; 28:1833. [PMID: 36838817 PMCID: PMC9965590 DOI: 10.3390/molecules28041833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 01/03/2023] [Accepted: 01/17/2023] [Indexed: 02/17/2023] Open
Abstract
The oral delivery system is very important and plays a significant role in increasing the solubility of drugs, which eventually will increase their absorption by the digestive system and enhance the drug bioactivity. This study was conducted to synthesize a novel curcumin nano lipid carrier (NLC) and use it as a drug carrier with the help of computational molecular docking to investigate its solubility in different solid and liquid lipids to choose the optimum lipids candidate for the NLCs formulation and avoid the ordinary methods that consume more time, materials, cost, and efforts during laboratory experiments. The antiviral activity of the formed curcumin-NLC against SARS-CoV-2 (COVID-19) was assessed through a molecular docking study of curcumin's affinity towards the host cell receptors. The novel curcumin drug carrier was synthesized as NLC using a hot and high-pressure homogenization method. Twenty different compositions of the drug carrier (curcumin nano lipid) were synthesized and characterized using different physicochemical techniques such as UV-Vis, FTIR, DSC, XRD, particle size, the zeta potential, and AFM. The in vitro and ex vivo studies were also conducted to test the solubility and the permeability of the 20 curcumin-NLC formulations. The NLC as a drug carrier shows an enormous enhancement in the solubility and permeability of the drug.
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Affiliation(s)
| | - Palanirajan Vijayaraj Kumar
- Faculty of Pharmaceutical Sciences, Department of Pharmaceutical Technology, UCSI University, Jalan Menara Gading, Taman Connaught, Cheras, Kuala Lumpur 56000, Malaysia
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2-Arylmelatonin analogues: Probing the 2-phenyl binding pocket of melatonin MT 1 and MT 2 receptors. Eur J Med Chem 2022; 243:114762. [PMID: 36150258 DOI: 10.1016/j.ejmech.2022.114762] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/29/2022] [Accepted: 09/07/2022] [Indexed: 11/21/2022]
Abstract
In crystal structures of melatonin MT1 and MT2 receptors, a lipophilic subpocket has been characterized which accommodates the phenyl ring of the potent agonist 2-phenylmelatonin. This subpocket appears a key structural element to achieve high binding affinity and selectivity for the MT2 receptor. A series of 2-arylindole ligands was synthesized to probe the requirements for the optimal occupation and interaction with the 2-phenyl binding pocket. Thermodynamic integration simulations applied to MT1 and MT2 receptors in complex with the α-naphthyl derivative provided a rationale for the MT2-selectivity and investigation on the binding mode of a couple of atropisomers allowed to define the available space and arrangement of substituents inside the subpocket. Interestingly, more hydrophilic 2-aza-substituted compounds displayed high binding affinity and molecular dynamics simulations highlighted polar interaction with residues from the subpocket that could be responsible for their potency.
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Somalo-Barranco G, Serra C, Lyons D, Piggins HD, Jockers R, Llebaria A. Design and Validation of the First Family of Photo-Activatable Ligands for Melatonin Receptors. J Med Chem 2022; 65:11229-11240. [PMID: 35930058 PMCID: PMC9421648 DOI: 10.1021/acs.jmedchem.2c00717] [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] [Indexed: 01/19/2023]
Abstract
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Melatonin is a neurohormone released in a circadian manner
with
peak levels at night. Melatonin mediates its effects mainly through
G protein-coupled MT1 and MT2 receptors. Drugs
acting on melatonin receptors are indicated for circadian rhythm-
and sleep-related disorders. Tools to study the activation of these
receptors with high temporal resolution are lacking. Here, we synthesized
a family of light-activatable caged compounds by attaching o-nitrobenzyl (o-NB) or coumarin photocleavable
groups to melatonin indolic nitrogen. All caged compounds showed the
expected decrease in binding affinity for MT1 and MT2. The o-NB derivative MCS-0382 showed the
best uncaging and biological properties, with 250-fold increase in
affinity and potency upon illumination. Generation of melatonin from
MCS-0382 was further demonstrated by its ability to modulate the excitation
of SCN neurons in rat brain slices. MCS-0382 is available to study
melatonin effects in a temporally controlled manner in cellular and
physiological settings.
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Affiliation(s)
- Gloria Somalo-Barranco
- Université de Paris, Institut Cochin, INSERM, CNRS, F-75014 Paris, France.,MCS, Laboratory of Medicinal Chemistry & Synthesis, Department of Biological Chemistry, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), 08034 Barcelona, Spain
| | - Carme Serra
- MCS, Laboratory of Medicinal Chemistry & Synthesis, Department of Biological Chemistry, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), 08034 Barcelona, Spain.,SIMChem, Synthesis of High Added Value Molecules, Institute of Advanced Chemistry of Catalonia (IQAC-CSIC), 08034 Barcelona, Spain
| | - David Lyons
- School of Physiology, Pharmacology and Neuroscience, Faculty of Life Sciences, University of Bristol, BS8 1TD Bristol, U.K
| | - Hugh D Piggins
- School of Physiology, Pharmacology and Neuroscience, Faculty of Life Sciences, University of Bristol, BS8 1TD Bristol, U.K
| | - Ralf Jockers
- Université de Paris, Institut Cochin, INSERM, CNRS, F-75014 Paris, France
| | - Amadeu Llebaria
- MCS, Laboratory of Medicinal Chemistry & Synthesis, Department of Biological Chemistry, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), 08034 Barcelona, Spain
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