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Sharma A, Sharma M, Bharate SB. N-Benzyl piperidine Fragment in Drug Discovery. ChemMedChem 2024:e202400384. [PMID: 38924676 DOI: 10.1002/cmdc.202400384] [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: 05/21/2024] [Revised: 06/22/2024] [Accepted: 06/26/2024] [Indexed: 06/28/2024]
Abstract
The N-benzyl piperidine (N-BP) structural motif is commonly employed in drug discovery due to its structural flexibility and three-dimensional nature. Medicinal chemists frequently utilize the N-BP motif as a versatile tool to fine-tune both efficacy and physicochemical properties in drug development. It provides crucial cation-π interactions with the target protein and also serves as a platform for optimizing stereochemical aspects of potency and toxicity. This motif is found in numerous approved drugs and clinical/preclinical candidates. This review focuses on the applications of the N-BP motif in drug discovery campaigns, emphasizing its role in imparting medicinally relevant properties. The review also provides an overview of approved drugs, the clinical and preclinical pipeline, and discusses its utility for specific therapeutic targets and indications, along with potential challenges.
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Affiliation(s)
- Ankita Sharma
- Natural Products & Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Mohit Sharma
- Natural Products & Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Sandip B Bharate
- Natural Products & Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India
- Department of Natural Products & Medicinal Chemistry, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad, 500007, India
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Zampieri D, Fortuna S, Romano M, Amata E, Dichiara M, Marrazzo A, Pasquinucci L, Turnaturi R, Mamolo MG. Design, synthesis and biological evaluation of novel aminopropylcarboxamide derivatives as sigma ligands. Bioorg Med Chem Lett 2022; 72:128860. [PMID: 35724925 DOI: 10.1016/j.bmcl.2022.128860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 06/12/2022] [Accepted: 06/13/2022] [Indexed: 11/20/2022]
Abstract
In our continuing effort to develop novel sigma receptor (SR) ligands, we present the design, synthesis and binding studies of a small library of aminopropylcarboxamide derivatives, obtained from a deconstruction of the piperidine ring of previously synthesized piperidine-based compounds. The best results were achieved with benzofuran (5c, 5g) and quinoline (5a, 5e) derivatives. These compounds revealed the highest affinity for both receptor subtypes. In particular, the 3,4-dimethoxyphenyl derivatives 5e and 5g showed the highest selectivity profile for S2R, especially the quinoline derivative 5e exhibited a 35-fold higher affinity for S2R subtype. The cytotoxic activity of aforementioned compounds was evaluated against SKBR3 and MCF7 cell lines, widely used for breast cancer studies. Whereas the potency of 5g was similar that of Siramesine and Haloperidol in both cell lines, compounds 5a, 5c and 5e exhibited a potency at least comparable to that of Haloperidol in SKBR3 cells. A molecular modelling evaluation towards the S2R binding site, confirmed the strong interaction of compound 5e thus justifying its highest S2R affinity.
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Affiliation(s)
- Daniele Zampieri
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy.
| | - Sara Fortuna
- Italian Institute of Technology (IIT), Via E. Melen 83, 16152 Genova, Italy
| | - Maurizio Romano
- Department of Life Sciences, University of Trieste, Via Valerio 28/1, 34127 Trieste, Italy
| | - Emanuele Amata
- Department of Drug and Health Sciences, University of Catania, Viale Doria 6, 95125 Catania, Italy
| | - Maria Dichiara
- Department of Drug and Health Sciences, University of Catania, Viale Doria 6, 95125 Catania, Italy
| | - Agostino Marrazzo
- Department of Drug and Health Sciences, University of Catania, Viale Doria 6, 95125 Catania, Italy
| | - Lorella Pasquinucci
- Department of Drug and Health Sciences, University of Catania, Viale Doria 6, 95125 Catania, Italy
| | - Rita Turnaturi
- Department of Drug and Health Sciences, University of Catania, Viale Doria 6, 95125 Catania, Italy
| | - Maria Grazia Mamolo
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
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Ye N, Qin W, Tian S, Xu Q, Wold EA, Zhou J, Zhen XC. Small Molecules Selectively Targeting Sigma-1 Receptor for the Treatment of Neurological Diseases. J Med Chem 2020; 63:15187-15217. [PMID: 33111525 DOI: 10.1021/acs.jmedchem.0c01192] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The sigma-1 (σ1) receptor, an enigmatic protein originally classified as an opioid receptor subtype, is now understood to possess unique structural and functional features of its own and play critical roles to widely impact signaling transduction by interacting with receptors, ion channels, lipids, and kinases. The σ1 receptor is implicated in modulating learning, memory, emotion, sensory systems, neuronal development, and cognition and accordingly is now an actively pursued drug target for various neurological and neuropsychiatric disorders. Evaluation of the five selective σ1 receptor drug candidates (pridopidine, ANAVEX2-73, SA4503, S1RA, and T-817MA) that have entered clinical trials has shown that reaching clinical approval remains an evasive and important goal. This review provides up-to-date information on the selective targeting of σ1 receptors, including their history, function, reported crystal structures, and roles in neurological diseases, as well as a useful collation of new chemical entities as σ1 selective orthosteric ligands or allosteric modulators.
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Affiliation(s)
- Na Ye
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, China
| | - Wangzhi Qin
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, China
| | - Sheng Tian
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, China
| | - Qingfeng Xu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, China
| | - Eric A Wold
- Chemical Biology Program, Department of Pharmacology and Toxicology, and Center for Addiction Research, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Jia Zhou
- Chemical Biology Program, Department of Pharmacology and Toxicology, and Center for Addiction Research, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Xue-Chu Zhen
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, China
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Zampieri D, Fortuna S, Calabretti A, Romano M, Menegazzi R, Schepmann D, Wünsch B, Mamolo MG. Synthesis, Cytotoxicity Evaluation, and Computational Insights of Novel 1,4-Diazepane-Based Sigma Ligands. ACS Med Chem Lett 2020; 11:651-656. [PMID: 32435366 DOI: 10.1021/acsmedchemlett.9b00524] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 12/16/2019] [Indexed: 01/01/2023] Open
Abstract
Among several potential applications, sigma receptor ligands can be used as antipsychotics, antiamnesics, and against other neurodegenerative disorders as well as neuroprotective agents. We present herein a new series of diazepane-containing derivatives as σR ligands obtained by a conformational expansion approach of our previously synthesized piperidine-based compounds. The best results were reached by benzofurane 2c, 3c and quinoline 2d, 3d-substituted diazepane derivatives, which showed the highest σR affinity. The cytotoxic activities of synthesized compounds were evaluated against two cancer cell lines, and the results indicated that none of the compounds induced significant toxicity in these cells. We also evaluated the antioxidant activity by radical scavenging capacity of our best compounds on ABTS and H2O2. The results obtained reveal that our new derivatives possess an excellent antioxidant profile and could be protective for the cells. Overall, the benzofurane derivative 2c due to its strong interaction with the active site of the receptor, as confirmed by molecular dynamic simulations, emerged as the optimum compound with high σ1R affinity, low cytotoxicity, and a potent antioxidant activity.
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Affiliation(s)
- Daniele Zampieri
- Department of Chemical and Pharmaceutical Sciences, P.le Europa 1-Via Giorgieri 1, University of Trieste, 34127 Trieste, Italy
| | - Sara Fortuna
- Department of Chemical and Pharmaceutical Sciences, P.le Europa 1-Via Giorgieri 1, University of Trieste, 34127 Trieste, Italy
| | - Antonella Calabretti
- Department of Chemical and Pharmaceutical Sciences, P.le Europa 1-Via Giorgieri 1, University of Trieste, 34127 Trieste, Italy
| | - Maurizio Romano
- Department of Life Sciences, Via Valerio 28/1, University of Trieste, 34127 Trieste, Italy
| | - Renzo Menegazzi
- Department of Life Sciences, Via Valerio 28/1, University of Trieste, 34127 Trieste, Italy
| | - Dirk Schepmann
- Institute of Pharmaceutical and Medicinal Chemistry, Corrensstraße 48, 48149 Münster, Germany
| | - Bernhard Wünsch
- Institute of Pharmaceutical and Medicinal Chemistry, Corrensstraße 48, 48149 Münster, Germany
| | - Maria Grazia Mamolo
- Department of Chemical and Pharmaceutical Sciences, P.le Europa 1-Via Giorgieri 1, University of Trieste, 34127 Trieste, Italy
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Zampieri D, Romano M, Menegazzi R, Mamolo MG. New piperidine-based derivatives as sigma receptor ligands. Synthesis and pharmacological evaluation. Bioorg Med Chem Lett 2018; 28:3206-3209. [DOI: 10.1016/j.bmcl.2018.08.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 08/10/2018] [Accepted: 08/13/2018] [Indexed: 01/27/2023]
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Ismaili L, Refouvelet B, Benchekroun M, Brogi S, Brindisi M, Gemma S, Campiani G, Filipic S, Agbaba D, Esteban G, Unzeta M, Nikolic K, Butini S, Marco-Contelles J. Multitarget compounds bearing tacrine- and donepezil-like structural and functional motifs for the potential treatment of Alzheimer's disease. Prog Neurobiol 2017; 151:4-34. [DOI: 10.1016/j.pneurobio.2015.12.003] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Revised: 11/11/2015] [Accepted: 12/11/2015] [Indexed: 01/16/2023]
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Abstract
This chapter presents the three-dimensional (3D) model of the Sigma1 receptor protein as obtained from homology modeling techniques. We show the applicability of this structure to docking-based virtual screening and discuss combined in silico/in vitro mutagenesis studies performed to validate the structural features of the Sigma1 receptor model and to qualify/quantify the prominent role of specific amino acid residues in ligand binding. The validation of the virtual 3D Sigma1 receptor model and its reliable applicability to docking-based virtual screening is of significance for rational ligand design, even in light of the recently reported crystal structure for the Sigma1 receptor.
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Affiliation(s)
- Erik Laurini
- Molecular Simulation Engineering (MOSE) Laboratory, Department of Engineering and Architecture (DEA), University of Trieste, Via Valerio 6, 34127, Trieste, Italy
| | - Domenico Marson
- Molecular Simulation Engineering (MOSE) Laboratory, Department of Engineering and Architecture (DEA), University of Trieste, Via Valerio 6, 34127, Trieste, Italy
| | - Maurizio Fermeglia
- Molecular Simulation Engineering (MOSE) Laboratory, Department of Engineering and Architecture (DEA), University of Trieste, Via Valerio 6, 34127, Trieste, Italy
| | - Sabrina Pricl
- Molecular Simulation Engineering (MOSE) Laboratory, Department of Engineering and Architecture (DEA), University of Trieste, Via Valerio 6, 34127, Trieste, Italy.
- National Interuniversity Consortium for Material Science and Technology (INSTM), Research Unit MOSE-DEA, University of Trieste, Via Valerio 6, 34127, Trieste, Italy.
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Computer-assisted design, synthesis, binding and cytotoxicity assessments of new 1-(4-(aryl(methyl)amino)butyl)-heterocyclic sigma 1 ligands. Eur J Med Chem 2016; 121:712-726. [DOI: 10.1016/j.ejmech.2016.06.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 05/30/2016] [Accepted: 06/01/2016] [Indexed: 11/21/2022]
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Briguglio I, Loddo R, Laurini E, Fermeglia M, Piras S, Corona P, Giunchedi P, Gavini E, Sanna G, Giliberti G, Ibba C, Farci P, La Colla P, Pricl S, Carta A. Synthesis, cytotoxicity and antiviral evaluation of new series of imidazo[4,5-g]quinoline and pyrido[2,3-g]quinoxalinone derivatives. Eur J Med Chem 2015; 105:63-79. [DOI: 10.1016/j.ejmech.2015.10.002] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Revised: 10/01/2015] [Accepted: 10/03/2015] [Indexed: 10/23/2022]
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Zampieri D, Laurini E, Vio L, Fermeglia M, Pricl S, Wünsch B, Schepmann D, Mamolo MG. Improving selectivity preserving affinity: new piperidine-4-carboxamide derivatives as effective sigma-1-ligands. Eur J Med Chem 2015; 90:797-808. [PMID: 25528334 DOI: 10.1016/j.ejmech.2014.12.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Revised: 11/19/2014] [Accepted: 12/11/2014] [Indexed: 10/24/2022]
Abstract
We report the design, synthesis and binding evaluation against σ1 and σ2 receptors of a series of new piperidine-4-carboxamide derivatives variously substituted on the amide nitrogen atom. Specifically, we assessed the effects exerted on σ receptor affinity by substituting the N-benzylcarboxamide group present on a series of compounds previously synthesized in our laboratory with different cyclic or linear moieties. The synthesized compounds 2a-o were tested to estimate their affinity and selectivity toward σ1 and σ2 receptors. Very high σ1 affinity (Ki = 3.7 nM) and Kiσ2/Kiσ1 selectivity ratio (351) were found for the tetrahydroquinoline derivative 2k, featuring a 4-chlorobenzyl moiety linked to the piperidine nitrogen atom.
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Affiliation(s)
- Daniele Zampieri
- Department of Chemistry & Pharmaceutical Sciences, Piazzale Europa 1, University of Trieste, 34127 Trieste, Italy.
| | - Erik Laurini
- Molecular Simulation Engineering (MOSE) Laboratory, DI3, Piazzale Europa 1, University of Trieste, 34127 Trieste, Italy
| | - Luciano Vio
- Department of Chemistry & Pharmaceutical Sciences, Piazzale Europa 1, University of Trieste, 34127 Trieste, Italy
| | - Maurizio Fermeglia
- Molecular Simulation Engineering (MOSE) Laboratory, DI3, Piazzale Europa 1, University of Trieste, 34127 Trieste, Italy
| | - Sabrina Pricl
- Molecular Simulation Engineering (MOSE) Laboratory, DI3, Piazzale Europa 1, University of Trieste, 34127 Trieste, Italy; National Interuniversity Consortium for Material Science and Technology (INSTM), Research Unit MOSE-DEA, University of Trieste, Trieste, Italy.
| | - Bernhard Wünsch
- Department of Pharmaceutical and Medicinal Chemistry, Corrensstrasse 48, 48149 Münster, Germany
| | - Dirk Schepmann
- Department of Pharmaceutical and Medicinal Chemistry, Corrensstrasse 48, 48149 Münster, Germany
| | - Maria Grazia Mamolo
- Department of Chemistry & Pharmaceutical Sciences, Piazzale Europa 1, University of Trieste, 34127 Trieste, Italy
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