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Antoniou M, Papavasileiou KD, Melagraki G, Dondero F, Lynch I, Afantitis A. Development of a Robust Read-Across Model for the Prediction of Biological Potency of Novel Peroxisome Proliferator-Activated Receptor Delta Agonists. Int J Mol Sci 2024; 25:5216. [PMID: 38791255 PMCID: PMC11121726 DOI: 10.3390/ijms25105216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 05/02/2024] [Accepted: 05/03/2024] [Indexed: 05/26/2024] Open
Abstract
A robust predictive model was developed using 136 novel peroxisome proliferator-activated receptor delta (PPARδ) agonists, a distinct subtype of lipid-activated transcription factors of the nuclear receptor superfamily that regulate target genes by binding to characteristic sequences of DNA bases. The model employs various structural descriptors and docking calculations and provides predictions of the biological activity of PPARδ agonists, following the criteria of the Organization for Economic Co-operation and Development (OECD) for the development and validation of quantitative structure-activity relationship (QSAR) models. Specifically focused on small molecules, the model facilitates the identification of highly potent and selective PPARδ agonists and offers a read-across concept by providing the chemical neighbours of the compound under study. The model development process was conducted on Isalos Analytics Software (v. 0.1.17) which provides an intuitive environment for machine-learning applications. The final model was released as a user-friendly web tool and can be accessed through the Enalos Cloud platform's graphical user interface (GUI).
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Affiliation(s)
- Maria Antoniou
- Department of Chemoinformatics, NovaMechanics Ltd., Nicosia 1046, Cyprus; (M.A.); (K.D.P.)
- Department of ChemoInformatics, NovaMechanics MIKE, 18545 Piraeus, Greece
- Entelos Institute, Larnaca 6059, Cyprus; (F.D.); (I.L.)
| | - Konstantinos D. Papavasileiou
- Department of Chemoinformatics, NovaMechanics Ltd., Nicosia 1046, Cyprus; (M.A.); (K.D.P.)
- Department of ChemoInformatics, NovaMechanics MIKE, 18545 Piraeus, Greece
- Entelos Institute, Larnaca 6059, Cyprus; (F.D.); (I.L.)
| | - Georgia Melagraki
- Division of Physical Sciences & Applications, Hellenic Military Academy, 16672 Vari, Greece;
| | - Francesco Dondero
- Entelos Institute, Larnaca 6059, Cyprus; (F.D.); (I.L.)
- Department of Science and Technological Innovation, Università del Piemonte Orientale, 15121 Alessandria, Italy
| | - Iseult Lynch
- Entelos Institute, Larnaca 6059, Cyprus; (F.D.); (I.L.)
- School of Geography, Earth and Environmental Sciences, University of Birmingham Edgbaston, Birmingham B15 2TT, UK
| | - Antreas Afantitis
- Department of Chemoinformatics, NovaMechanics Ltd., Nicosia 1046, Cyprus; (M.A.); (K.D.P.)
- Department of ChemoInformatics, NovaMechanics MIKE, 18545 Piraeus, Greece
- Entelos Institute, Larnaca 6059, Cyprus; (F.D.); (I.L.)
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Zhang W, Chen Z, Jiang YX, Liao LL, Wang W, Ye JH, Yu DG. Arylcarboxylation of unactivated alkenes with CO 2 via visible-light photoredox catalysis. Nat Commun 2023; 14:3529. [PMID: 37316537 DOI: 10.1038/s41467-023-39240-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 05/31/2023] [Indexed: 06/16/2023] Open
Abstract
Photocatalytic carboxylation of alkenes with CO2 is a promising and sustainable strategy to synthesize high value-added carboxylic acids. However, it is challenging and rarely investigated for unactivated alkenes due to their low reactivities. Herein, we report a visible-light photoredox-catalyzed arylcarboxylation of unactivated alkenes with CO2, delivering a variety of tetrahydronaphthalen-1-ylacetic acids, indan-1-ylacetic acids, indolin-3-ylacetic acids, chroman-4-ylacetic acids and thiochroman-4-ylacetic acids in moderate-to-good yields. This reaction features high chemo- and regio-selectivities, mild reaction conditions (1 atm, room temperature), broad substrate scope, good functional group compatibility, easy scalability and facile derivatization of products. Mechanistic studies indicate that in situ generation of carbon dioxide radical anion and following radical addition to unactivated alkenes might be involved in the process.
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Affiliation(s)
- Wei Zhang
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu, 610064, China
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Zhen Chen
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu, 610064, China
| | - Yuan-Xu Jiang
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu, 610064, China
| | - Li-Li Liao
- School of Chemistry and Chemical Engineering, Chongqing University, Chongqing, 400030, P. R. China
| | - Wei Wang
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu, 610064, China
| | - Jian-Heng Ye
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu, 610064, China.
| | - Da-Gang Yu
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu, 610064, China.
- State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin, 300071, P. R. China.
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Wang H, Huang H, Gong C, Diao Y, Chen J, Wu SH, Wang L. Nickel-Catalyzed Chemo- and Regioselective Benzylarylation of Unactivated Alkenes with o-Bromobenzyl Chlorides. Org Lett 2021; 24:328-333. [PMID: 34958584 DOI: 10.1021/acs.orglett.1c03991] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Chemo- and regioselectively nickel-catalyzed reductive benzylarylation of unactivated alkenes with o-bromobenzyl chlorides is disclosed herein, in which electrophiles participate through a single-component double-site approach. Moreover, its utility is underscored by the concise synthesis of bioactive Indane compounds and postreaction functionalizations leading to structurally diverse scaffolds. Preliminary mechanistic investigations suggest a radical chain reaction mechanism.
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Affiliation(s)
- Hailong Wang
- School of Medicine, Huaqiao University, Quanzhou 362021, P. R. China
| | - Haichao Huang
- School of Medicine, Huaqiao University, Quanzhou 362021, P. R. China
| | - Chao Gong
- School of Medicine, Huaqiao University, Quanzhou 362021, P. R. China
| | - Yong Diao
- School of Medicine, Huaqiao University, Quanzhou 362021, P. R. China
| | - Jianmei Chen
- School of Medicine, Huaqiao University, Quanzhou 362021, P. R. China
| | - Si-Hai Wu
- School of Medicine, Huaqiao University, Quanzhou 362021, P. R. China
| | - Lianhui Wang
- School of Medicine, Huaqiao University, Quanzhou 362021, P. R. China
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Structure-based virtual screening and discovery of New PPARδ/γ dual agonist and PPARδ and γ agonists. PLoS One 2015; 10:e0118790. [PMID: 25767888 PMCID: PMC4358979 DOI: 10.1371/journal.pone.0118790] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 12/16/2014] [Indexed: 12/13/2022] Open
Abstract
Peroxisome proliferator-activated receptors (PPARs) are involved in the control of carbohydrate and lipid metabolism and are considered important targets to treat diabetes mellitus and metabolic syndrome. The available PPAR ligands have several side effects leading to health risks justifying the search for new bioactive ligands to activate the PPAR subtypes, in special PPARδ, the less studied PPAR isoform. Here, we used a structure-based virtual screening protocol in order to find out new PPAR ligands. From a lead-like subset of purchasable compounds, we identified 5 compounds with potential PPAR affinity and, from preliminary in vitro assays, 4 of them showed promising biological activity. Therefore, from our in silico and in vitro protocols, new PPAR ligands are potential candidates to treat metabolic diseases.
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Wang XJ, Zhang J, Wang SQ, Xu WR, Cheng XC, Wang RL. Identification of novel multitargeted PPARα/γ/δ pan agonists by core hopping of rosiglitazone. DRUG DESIGN DEVELOPMENT AND THERAPY 2014; 8:2255-62. [PMID: 25422585 PMCID: PMC4232041 DOI: 10.2147/dddt.s70383] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The thiazolidinedione class peroxisome proliferator-activated receptor gamma (PPARγ) agonists are restricted in clinical use as antidiabetic agents because of side effects such as edema, weight gain, and heart failure. The single and selective agonism of PPARγ is the main cause of these side effects. Multitargeted PPARα/γ/δ pan agonist development is the hot topic in the antidiabetic drug research field. In order to identify PPARα/γ/δ pan agonists, a compound database was established by core hopping of rosiglitazone, which was then docked into a PPARα/γ/δ active site to screen out a number of candidate compounds with a higher docking score and better interaction with the active site. Further, absorption, distribution, metabolism, excretion, and toxicity prediction was done to give eight compounds. Molecular dynamics simulation of the representative Cpd#1 showed more favorable binding conformation for PPARs receptor than the original ligand. Cpd#1 could act as a PPARα/γ/δ pan agonist for novel antidiabetic drug research.
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Affiliation(s)
- Xue-Jiao Wang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, People's Republic of China
| | - Jun Zhang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, People's Republic of China
| | - Shu-Qing Wang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, People's Republic of China
| | - Wei-Ren Xu
- Tianjin Key Laboratory of Molecular Design and Drug Discovery, Tianjin Institute of Pharmaceutical Research, Tianjin, People's Republic of China
| | - Xian-Chao Cheng
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, People's Republic of China
| | - Run-Ling Wang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, People's Republic of China
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Schumann M, Armen RS. Identification of distant drug off-targets by direct superposition of binding pocket surfaces. PLoS One 2013; 8:e83533. [PMID: 24391782 PMCID: PMC3877058 DOI: 10.1371/journal.pone.0083533] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Accepted: 11/04/2013] [Indexed: 01/23/2023] Open
Abstract
Correctly predicting off-targets for a given molecular structure, which would have the ability to bind a large range of ligands, is both particularly difficult and important if they share no significant sequence or fold similarity with the respective molecular target ("distant off-targets"). A novel approach for identification of off-targets by direct superposition of protein binding pocket surfaces is presented and applied to a set of well-studied and highly relevant drug targets, including representative kinases and nuclear hormone receptors. The entire Protein Data Bank is searched for similar binding pockets and convincing distant off-target candidates were identified that share no significant sequence or fold similarity with the respective target structure. These putative target off-target pairs are further supported by the existence of compounds that bind strongly to both with high topological similarity, and in some cases, literature examples of individual compounds that bind to both. Also, our results clearly show that it is possible for binding pockets to exhibit a striking surface similarity, while the respective off-target shares neither significant sequence nor significant fold similarity with the respective molecular target ("distant off-target").
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Affiliation(s)
- Marcel Schumann
- Department of Pharmaceutical Sciences, School of Pharmacy, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
| | - Roger S. Armen
- Department of Pharmaceutical Sciences, School of Pharmacy, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
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Garcia TS, Silva DC, Gertrudes JC, Maltarollo VG, Honorio KM. Molecular features related to the binding mode of PPARδ agonists from QSAR and docking analyses. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2013; 24:157-173. [PMID: 23282254 DOI: 10.1080/1062936x.2012.751453] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Diabetes affects approximately 4% of world's population and metabolic syndrome has been directly related to obesity. There is a class of nuclear receptors, peroxisome proliferator-activated receptors (PPARs), which controls the metabolism of carbohydrates and lipids. It has been considered an attractive target to treat diabetes and metabolic syndrome. Accordingly, the primary objective of this study was to employ molecular modelling techniques to understand the factors involved in PPARδ activation. The QSAR models obtained showed good internal and external consistency and presented good validation coefficients (QSAR: q(2) = 0.83, r(2) = 0.87; HQSAR: q(2) = 0.73, r(2) = 0.90; CoMFA: q(2) = 0.88, r(2) = 0.94). The selected properties and the contour maps described the possible interactions between the PPARδ receptor and its agonists. From these findings, it is possible to propose molecular modifications to design new compounds with improved biological properties.
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Affiliation(s)
- T S Garcia
- School of Arts, Sciences and Humanities, University of São Paulo, São Paulo, Brazil
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Role of physicochemical properties in the activation of peroxisome proliferator-activated receptor δ. J Mol Model 2011; 17:2549-58. [DOI: 10.1007/s00894-010-0935-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2010] [Accepted: 12/09/2010] [Indexed: 02/07/2023]
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Theoretical study on the molecular and electronic properties of some substances used for diabetes mellitus treatment. J Mol Model 2009; 16:799-804. [DOI: 10.1007/s00894-009-0627-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2009] [Accepted: 11/15/2009] [Indexed: 10/20/2022]
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Lather V, Fernandes M. QSAR Models for Prediction of PPARδ Agonistic Activity of Indanylacetic Acid Derivatives. ACTA ACUST UNITED AC 2009. [DOI: 10.1002/qsar.200810092] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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