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Le Roch M, Renault J, Argouarch G, Lenci E, Trabocchi A, Roisnel T, Gouault N, Lalli C. Synthesis and Chemoinformatic Analysis of Fluorinated Piperidines as 3D Fragments for Fragment-Based Drug Discovery. J Org Chem 2024; 89:4932-4946. [PMID: 38451837 DOI: 10.1021/acs.joc.4c00143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2024]
Abstract
The concise synthesis of a small library of fluorinated piperidines from readily available dihydropyridinone derivatives has been described. The effect of the fluorination on different positions has then been evaluated by chemoinformatic tools. In particular, the compounds' pKa's have been calculated, revealing that the fluorine atoms notably lowered their basicity, which is correlated to the affinity for hERG channels resulting in cardiac toxicity. The "lead-likeness" and three-dimensionality have also been evaluated to assess their ability as useful fragments for drug design. A random screening on a panel of representative proteolytic enzymes was then carried out and revealed that one scaffold is recognized by the catalytic pocket of 3CLPro (main protease of SARS-CoV-2 coronavirus).
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Affiliation(s)
- Myriam Le Roch
- Univ Rennes, CNRS, ISCR-UMR 6226, Rennes F-35000, France
| | | | | | - Elena Lenci
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 13, Sesto Fiorentino, Florence 50019, Italy
| | - Andrea Trabocchi
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 13, Sesto Fiorentino, Florence 50019, Italy
| | - Thierry Roisnel
- Univ Rennes, Centre de Diffractométrie X (CDIFX), ISCR-UMR 6226, Rennes F-35000, France
| | | | - Claudia Lalli
- Univ Rennes, CNRS, ISCR-UMR 6226, Rennes F-35000, France
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Baldini L, Lenci E, Faggi C, Trabocchi A. Identification of BACE-1 inhibitors through directed C(sp 3)-H activation on 5-oxo-pyrrolidine-3-carboxylic acid derivatives. Org Biomol Chem 2024; 22:2754-2763. [PMID: 38488214 DOI: 10.1039/d3ob02117c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Convenient synthesis of stereochemically dense 5-oxo-pyrrolidines was obtained from succinic anyhdride and imines by combining the Castagnoli-Cushman reaction with directed Pd-catalyzed C(sp3)-H functionalization, taking advantage of the developing carboxylic group properly derivatized with 8-aminoquinoline as a directing group. These fully substituted 5-oxopyrrolidines were found to be able to inhibit BACE-1 enzyme with sub-micromolar activity, thanks to the interaction of the key aryl appendage introduced by C(sp3)-H activation within BACE-1 S2' subsite.
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Affiliation(s)
- Lorenzo Baldini
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 13, 50019 Sesto Fiorentino, Florence, Italy.
| | - Elena Lenci
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 13, 50019 Sesto Fiorentino, Florence, Italy.
| | - Cristina Faggi
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 13, 50019 Sesto Fiorentino, Florence, Italy.
| | - Andrea Trabocchi
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 13, 50019 Sesto Fiorentino, Florence, Italy.
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Iqbal S, Malik MZ, Pal D. Network-based identification of miRNAs and transcription factors and in silico drug screening targeting δ-secretase involved in Alzheimer's disease. Heliyon 2021; 7:e08502. [PMID: 34917801 PMCID: PMC8668832 DOI: 10.1016/j.heliyon.2021.e08502] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 09/27/2021] [Accepted: 11/25/2021] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND System medicine approaches have played a pivotal role in identifying novel disease networks especially in miRNA research. It is no wonder that miRNAs are implicated in multiple clinical conditions, allowing us to establish the hubs and nodes for network models of Alzheimer's Disease (AD). AD is an age-related, progressive, irreversible, and multifactorial neurodegenerative disorder characterized by cognitive and memory impairment and is the most common cause of dementia in older adults. Worldwide, around 50 million people have dementia, and there are nearly 10 million new cases every year. δ-secretase, also known as asparagine endopeptidase (AEP) or legumain (LGMN), is a lysosomal cysteine protease that cleaves peptide bonds C-terminally to asparagine residues in both amyloid precursor protein (APP) and tau, mediating the amyloid-β and tau pathology in AD. The patient's miRNA expression was found to be deregulated in the brain, extracellular fluid, blood plasma, and serum. METHODS Protein-Protein Interaction (PPI) networks of LGMN or δ-secretase were constructed using the Genemania database. Network Analyzer, a Cytoscape plugin, analyzed the network topological properties of LGMN. miRNAs related to Alzheimer's were extracted from the HMDD (Human microRNA Disease Database) and experimentally verified miRNA-gene interaction was obtained by searching miRWalk. Starbase v2.0 and miRanda were used for screening miRNA of LGMN genes. Moreover, to understand the regulatory mechanism in AD, we have screened major transcription factors of LGMN targeted genes using the Network Analyst 3.0, TRRUST (v2.0) server, and ENCODE. The Genotype-Tissue Expression (GTEx) and BEST tool were used to investigate the expression pattern of the LGMN gene. In parallel, we performed in-silico drug designing of the novel inhibitor scaffold of δ-secretase as powerful therapeutic targets by using the concept of scaffolds and frameworks. In this context, this study also aimed at identifying effective small molecule inhibitors targeting δ-secretase. RESULTS Among the 16 experimentally verified miRNAs, Network analysis of the LGMN and its associated miRNA identify novel hsa-miRNA-106a-5p and hsa-miRNA-34a-5p being more expressed in the brain. Our in silico high throughput screening, followed by XP docking revealed Oprea1 as the lead. Molecular dynamic simulations of the δ-secretase-docked complex have been carried out for a time period of 200 ns and revealed that Root Mean Square Deviation (RMSD) of the protein Cα-backbone with respect to its starting position increased to 1.20 Å for the first 25 ns of the trajectory and then became stable around 0.6 Å in the last 170 ns course of the simulation. The radius of gyration (RGYR) reveals that compactness was maintained till the end of simulations. CONCLUSION Network analysis of LGMN associated miRNAs lead to the identification of two novel miRNAs, being highly expressed in the brain. This study also lead to the identification and expression of 10 Transcription factors associated with LGMN. Expression Heatmap results show high and continuous expression of LGMN in most of the regions of the brain, especially in the frontal cortex. Further, in silico drug analysis led us to the identification of Oprea1 which could be taken for further investigation to explore its potential for AD therapy.
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Affiliation(s)
- Saleem Iqbal
- Department of Computational and Data Sciences, Indian Institute of Science, Bangalore 560012, India
| | - Md. Zubbair Malik
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Debnath Pal
- Department of Computational and Data Sciences, Indian Institute of Science, Bangalore 560012, India
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Abstract
![]()
Developing
drugs for the central nervous system (CNS) requires
fine chemical modifications, as a strict balance between size and
lipophilicity is necessary to improve the permeability through the
blood-brain barrier (BBB).
In this context, morpholine and its analogues represent valuable heterocycles,
due to their conformational and physicochemical properties. In fact,
the presence of a weak basic nitrogen atom and of an oxygen atom at
the opposite position provides a peculiar pKa value and a flexible conformation to the ring, thus allowing
it to take part in several lipophilic–hydrophilic interactions,
and to improve blood solubility and brain permeability of the overall
structure. In CNS-active compounds, morpholines are used (1) to enhance
the potency through molecular interactions, (2) to act as a scaffold
directing the appendages in the correct position, and (3) to modulate
pharmacokinetic/pharmacodynamic (PK/PD) properties. In this perspective,
selected morpholine-containing CNS drug candidates are discussed to
reveal the active pharmacophores accountable for the (1) modulation
of receptors involved in mood disorders and pain, (2) bioactivity
toward enzymes and receptors responsible for neurodegenerative diseases,
and (3) inhibition of enzymes involved in the pathology of CNS tumors.
The medicinal chemistry/pharmacological activity of morpholine derivatives
is discussed, in the effort to highlight the importance of morpholine
ring interactions in the active site of different targets, particularly
reporting binding features retrieved from PDB data, when available.
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Affiliation(s)
- Elena Lenci
- Department of Chemistry “Ugo Schiff”, University of Florence, via della Lastruccia 13, 50019 Sesto Fiorentino, Florence, Italy
| | - Lorenzo Calugi
- Department of Chemistry “Ugo Schiff”, University of Florence, via della Lastruccia 13, 50019 Sesto Fiorentino, Florence, Italy
| | - Andrea Trabocchi
- Department of Chemistry “Ugo Schiff”, University of Florence, via della Lastruccia 13, 50019 Sesto Fiorentino, Florence, Italy
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Synthesis of morpholine derivatives using the Castagnoli-Cushman reaction as BACE1 inhibitors: Unexpected binding activity of cyclic thioamides. Bioorg Med Chem Lett 2020; 30:127211. [PMID: 32354570 DOI: 10.1016/j.bmcl.2020.127211] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 04/20/2020] [Accepted: 04/23/2020] [Indexed: 01/18/2023]
Abstract
The Castagnoli-Cushman reaction between diglycolic anhydride and imines was applied for the synthesis of morpholine derivatives containing a thioamide or an amidino group. Enzyme inhibition assays towards BACE1 revealed an unexpected role of the cyclic thioamide group in providing inhibition in the micromolar range. Molecular docking calculations showed the thioamido group interacting with catalytic aspartic acid, and calculated BBB permeability indicated this molecular scaffold as a promising hit for further optimization.
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Lenci E, Menchi G, Saldívar-Gonzalez FI, Medina-Franco JL, Trabocchi A. Bicyclic acetals: biological relevance, scaffold analysis, and applications in diversity-oriented synthesis. Org Biomol Chem 2019; 17:1037-1052. [DOI: 10.1039/c8ob02808g] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The chemoinformatics analysis of fused, spiro, and bridged bicyclic acetals is instrumental for the DOS of natural product-inspired molecular collections.
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Affiliation(s)
- Elena Lenci
- Department of Chemistry “Ugo Schiff”
- University of Florence
- 50019 Sesto Fiorentino
- Italy
| | - Gloria Menchi
- Department of Chemistry “Ugo Schiff”
- University of Florence
- 50019 Sesto Fiorentino
- Italy
- Interdepartmental Center for Preclinical Development of Molecular Imaging (CISPIM)
| | - Fernanda I. Saldívar-Gonzalez
- School of Chemistry
- Department of Pharmacy
- Universidad Nacional Autónoma de México
- Avenida Universidad 3000
- Mexico City 04510
| | - José L. Medina-Franco
- School of Chemistry
- Department of Pharmacy
- Universidad Nacional Autónoma de México
- Avenida Universidad 3000
- Mexico City 04510
| | - Andrea Trabocchi
- Department of Chemistry “Ugo Schiff”
- University of Florence
- 50019 Sesto Fiorentino
- Italy
- Interdepartmental Center for Preclinical Development of Molecular Imaging (CISPIM)
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Ion GND, Mihai DP, Lupascu G, Nitulescu GM. Application of molecular framework-based data-mining method in the search for beta-secretase 1 inhibitors through drug repurposing. J Biomol Struct Dyn 2018; 37:3674-3685. [PMID: 30234434 DOI: 10.1080/07391102.2018.1526115] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Targeting beta-secretase 1, also known as beta-amyloid precursor protein-cleaving enzyme (BACE-1) for the inhibition of amyloid production, has been intensely studied in the last decades in the search for stopping Alzheimer's disease (AD) progression. The chances of finding a druggable BACE-1 inhibitor may be increased by drug repurposing, as this kind of molecules already fulfil certain requirements needed for further advancement. The study describes the development and application of a data-mining method based on molecular frameworks and descriptor values of tested BACE-1 inhibitors, suitable for filtering large compound databases, in order to find molecules with high potency against this protease. A total of 465 compounds extracted from the literature, tested against BACE-1, were analysed for finding molecular descriptor values and frameworks that ensure a high probability of strong inhibition. Resulting conclusions were used for filtering DrugBank database, containing ∼8700 approved and experimental drugs, obtaining 26 structures characterized by four major Bemis-Murcko frameworks: 2-[3-(2-cyclohexylethyl)cyclohexyl]-decahydronaphthalene, 3-(2-cyclohexylethyl)-1,1'-bi(cyclohexane), [5-(cyclohexylmethyl)-8-cyclopentyloctyl]cyclohexane and (3-cyclohexylcyclopentyl)cyclohexane. The compounds were further studied by molecular docking using the structure of the closed form of the enzyme, which revealed seven compounds already involved in trials targeting BACE-1 inhibition, confirming the method's specificity. The compounds that afforded the best binding energies were DB06925 (tyrosine-protein kinase inhibitor), DB12285 (Verubecestat) and DB08899 (Enzalutamide). Moreover, docking results indicated several other molecules with high in silico inhibitory potency that can be further studied for developing a potential treatment for AD. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Dragos Paul Mihai
- a Faculty of Pharmacy , Carol Davila University of Medicine and Pharmacy , Bucharest , Romania
| | - Gina Lupascu
- a Faculty of Pharmacy , Carol Davila University of Medicine and Pharmacy , Bucharest , Romania
| | - George Mihai Nitulescu
- a Faculty of Pharmacy , Carol Davila University of Medicine and Pharmacy , Bucharest , Romania
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Lenci E, Innocenti R, Menchi G, Trabocchi A. Diversity-Oriented Synthesis and Chemoinformatic Analysis of the Molecular Diversity of sp 3-Rich Morpholine Peptidomimetics. Front Chem 2018; 6:522. [PMID: 30425982 PMCID: PMC6218424 DOI: 10.3389/fchem.2018.00522] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 10/10/2018] [Indexed: 12/03/2022] Open
Abstract
Diversity-Oriented Synthesis (DOS) consists of generating structurally diverse compounds from a complexity-generating reaction followed by cyclization steps and appendage diversity. DOS has gathered interest to systematically explore the chemical space by generating high-quality small-molecule collections as probes to investigate biological pathways. The generation of heterocycles using amino acid and sugar derivatives as building blocks is a powerful approach to access chemical and geometrical diversity thanks to the high number of stereocenters and the polyfunctionality of such compounds. Our efforts in this field are focused on the generation of diversity-oriented molecules of peptidomimetic nature as a tool addressing protein-protein interactions, taking advantage of amino acid- and sugar-derived polyfunctional building blocks to be applied in couple-pair synthetic approaches. In this paper, the combination of diversity-oriented synthesis and chemoinformatics analysis of chemical space and molecular diversity of heterocyclic peptidomimetics are reported, with particular interest toward carbohydrate- and amino acid-derived morpholine scaffolds with a higher fraction of sp3 carbon atoms. Also, the chemoinformatic analysis of chemical space and molecular diversity of 186 morpholine peptidomimetics is outlined.
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Affiliation(s)
- Elena Lenci
- Department of Chemistry “Ugo Schiff”, University of Florence, Florence, Italy
| | | | | | - Andrea Trabocchi
- Department of Chemistry “Ugo Schiff”, University of Florence, Florence, Italy
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Gabr MT, Abdel-Raziq MS. Structure-based design, synthesis, and evaluation of structurally rigid donepezil analogues as dual AChE and BACE-1 inhibitors. Bioorg Med Chem Lett 2018; 28:2910-2913. [PMID: 30017317 DOI: 10.1016/j.bmcl.2018.07.019] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 07/09/2018] [Accepted: 07/10/2018] [Indexed: 11/15/2022]
Abstract
A new series of structurally rigid donepezil analogues was designed, synthesized and evaluated as potential multi-target-directed ligands (MTDLs) against neurodegenerative diseases. The investigated compounds 10-13 displayed dual AChE and BACE-1 inhibitory activities in comparison to donepezil, the FDA-approved drug. The hybrid compound 13 bearing 2-aminoquinoline scaffold exhibited potent AChE inhibition (IC50 value of 14.7 nM) and BACE-1 inhibition (IC50 value of 13.1 nM). Molecular modeling studies were employed to reveal potential dual binding mode of 13 to AChE and BACE-1. The effect of the investigated compounds on the viability of SH-SY5Y neuroblastoma cells and their ability to cross the blood-brain barrier (BBB) in PAMPA-BBB assay were further studied.
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Affiliation(s)
- Moustafa T Gabr
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt; Department of Chemistry, University of Iowa, Iowa City, IA 52242, USA.
| | - Mohammed S Abdel-Raziq
- Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt; School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia 4072, Queensland, Australia
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Zhao Y, Wang C, Hu Y, Wan B. Brønsted acid-catalyzed formal [5+2+1] cycloaddition of ynamides and isoxazoles with water: access to oxygen-bridged tetrahydro-1,4-oxazepines. Chem Commun (Camb) 2018; 54:3963-3966. [DOI: 10.1039/c8cc00881g] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The unique property of the Brønsted acid, as well as introducing a small amount of water, shows distinct chemoselectivity from the corresponding gold-catalyzed cycloadditions.
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Affiliation(s)
- Yingying Zhao
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian 116023
- China
- University of Chinese Academy of Sciences
| | - Chunxiang Wang
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian 116023
- China
| | - Yancheng Hu
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian 116023
- China
| | - Boshun Wan
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian 116023
- China
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