1
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Lavanya P, Davis G DJ. Chemo-structural diversity of anti-obesity compound database. J Mol Graph Model 2023; 120:108414. [PMID: 36702059 DOI: 10.1016/j.jmgm.2023.108414] [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: 08/18/2022] [Revised: 12/28/2022] [Accepted: 01/12/2023] [Indexed: 01/20/2023]
Abstract
Nature plays a major role in the development of new drugs which helps in preventing and treating human diseases. Anti-obesity compound database (AOCD) contains comprehensive information on all published small molecules from natural sources with anti-obesity potential targeting pancreatic lipase (PL), appetite suppressant (AS) and adipogenesis (AD). Presently the database contains 349 compounds isolated from 307 plants, 26 marine and 16 microbial sources. Users can query the AOCD database (https://aocd.swmd.co.in/) in several ways. The database was divided into three datasets (PL, AS and AD) to perform chemoinformatic analysis using Platform for Unified Molecular Analysis (PUMA), which were analyzed based on molecular descriptors, scaffold diversity and structural fingerprint diversity. Chemoinformatics study inferred the PL dataset has the highest diversity of compounds based on the Euclidean distance on molecular properties, scaffold diversity and pairwise similarity on fingerprint diversity. This study would hasten the process of anti-obesity drug discovery.
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Affiliation(s)
- Prabhakar Lavanya
- Department of Bioinformatics, Faculty of Engineering and Technology, Sri Ramachandra Institute of Higher Education and Research (DU), Chennai, India
| | - Dicky John Davis G
- Department of Bioinformatics, Faculty of Engineering and Technology, Sri Ramachandra Institute of Higher Education and Research (DU), Chennai, India.
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2
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Ahamed TKS, Muraleedharan K. A cheminformatic study on chemical space characterization and diversity analysis of 5-LOX inhibitors. J Mol Graph Model 2020; 100:107699. [PMID: 32799052 DOI: 10.1016/j.jmgm.2020.107699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 06/19/2020] [Accepted: 07/10/2020] [Indexed: 10/23/2022]
Abstract
The process of blocking 5-lipoxygenase (5-LOX) catalyzed leukotriene biosynthesis has been recognized for the past few decades as a promising therapeutic strategy for acute inflammatory, allergic, and respiratory diseases. Due to the toxicity effect of FDA approved 5-LOX inhibitor zileuton, novel 5-LOX inhibitors have been sought by the scientific community. As a result, a significant and relevant amount of information on the structure-activity of 5-LOX inhibitors has been released and stored in public databases. In this study, we aimed at the comprehensive cheminformatic characterization of the diversity and complexity of the chemical space of 5-LOX inhibitors and its activating protein FLAP inhibitors by comparing it with the Approved drug space and virtual LOX library. The visual representation of the property space indicates some compounds in the 5-LOX inhibitors space broaden the traditional medicinal space. The structural diversity of the databases is computed using complementary approaches, including Physicochemical Property (PCP) descriptors, molecular fingerprints, and molecular scaffold. With the apparent exception of approved drugs, the 5-LOX dataset shows more diversity compared to FLAP and LOX virtual library set. This study was able to identify the underlying patterns in the chemical and pharmacological properties space that were decisive for the drug discovery and development of 5-LOX inhibitors.
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Affiliation(s)
| | - K Muraleedharan
- Department of Chemistry, University of Calicut, Malappuram, 673635, India.
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3
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Sharma R. Data science-driven analyses of drugs inducing hypertension as an adverse effect. Mol Divers 2020; 25:801-810. [PMID: 32415493 DOI: 10.1007/s11030-020-10059-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 02/21/2020] [Indexed: 12/15/2022]
Abstract
The utilization of approved medication is a requisite to combat certain diseases for health; however, the undesirable adverse effects (AEs) due to medication are generally unavoidable. Hypertension is one of such AEs resulting from approved medication in which blood pressure in the arteries gets elevated and is a risk factor for several diseases including heart and kidney failure. HTs are the approved drugs that can cause hypertension as an AE. Here, the goal of the study is to investigate the structural and functional diversities of HTs. In our quest to unravel the structural parameters of the HTs, a systematic analysis of the HTs having a different number and type of ring systems was conducted. The cellular component, molecular function and biological processes adopted by the gene products were analyzed. Moreover, our systematically done analysis suggests that all the target families are active in a common pathway, that is, nerve transmission. A comparison of the selected structural and functional aspect of HTs with anti-hypertensives suggests that HTs follow certain structural and functional features in spite of many possibilities. Our study provides a promising methodology that considers the influence of structural diversity of AE causing agents on a functional perspective for precursory clinical decision making. This could be extended to explore the structural and functional trends that are adopted by agents causing certain diseases or AEs.
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Affiliation(s)
- Reetu Sharma
- CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad, 500007, India.
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4
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Medina-Franco JL, Cruz-Lemus Y, Percastre-Cruz Y. Chemoinformatic Resources for Organometallic Drug Discovery. ACTA ACUST UNITED AC 2020. [DOI: 10.4236/cmb.2020.101001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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5
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Cluster analysis to identify prominent patterns of anti-hypertensives: A three-tiered unsupervised learning approach. INFORMATICS IN MEDICINE UNLOCKED 2020. [DOI: 10.1016/j.imu.2020.100303] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
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6
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Systematic search for benzimidazole compounds and derivatives with antileishmanial effects. Mol Divers 2018; 22:779-790. [DOI: 10.1007/s11030-018-9830-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Accepted: 04/26/2018] [Indexed: 10/16/2022]
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7
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Grygorenko OO, Demenko D, Volochnyuk DM, Komarov IV. Following Ramachandran 2: exit vector plot (EVP) analysis of disubstituted saturated rings. NEW J CHEM 2018. [DOI: 10.1039/c7nj05015a] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
EVP analysis of common saturated rings revealed five regions (α–ε); only part of them corresponds to 3D molecular structures.
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Affiliation(s)
- Oleksandr O. Grygorenko
- Enamine Ltd (www.enamine.net)
- Kyiv 02066
- Ukraine
- National Taras Shevchenko University of Kyiv
- Kyiv 01601
| | | | - Dmitry M. Volochnyuk
- Enamine Ltd (www.enamine.net)
- Kyiv 02066
- Ukraine
- Institute of Organic Chemistry National Academy of Sciences of Ukraine
- Kyiv 02094
| | - Igor V. Komarov
- Enamine Ltd (www.enamine.net)
- Kyiv 02066
- Ukraine
- National Taras Shevchenko University of Kyiv
- Kyiv 01601
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8
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The potential role of in silico approaches to identify novel bioactive molecules from natural resources. Future Med Chem 2017; 9:1665-1686. [PMID: 28841048 DOI: 10.4155/fmc-2017-0124] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
In recent years, integration of in silico approaches to natural product (NP) research reawakened the declined interest in NP-based drug discovery efforts. In particular, advancements in cheminformatics enabled comparison of NP databases with contemporary small-molecule libraries in terms of molecular properties and chemical space localizations. Virtual screening and target fishing approaches were successful in recognizing the untold macromolecular targets for NPs to exploit the unmet therapeutic needs. Developments in molecular docking and scoring methods along with molecular dynamics enabled to predict the target-ligand interactions more accurately taking into consideration the remarkable structural complexity of NPs. Hence, innovative in silico strategies have contributed valuably to the NP research in drug discovery processes as reviewed herein. [Formula: see text].
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9
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González-Medina M, Medina-Franco JL. Platform for Unified Molecular Analysis: PUMA. J Chem Inf Model 2017; 57:1735-1740. [PMID: 28737911 DOI: 10.1021/acs.jcim.7b00253] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We introduce a free platform for chemoinformatic-based diversity analysis and visualization of chemical space of user supplied data sets. Platform for Unified Molecular Analysis (PUMA) integrates metrics used to characterize compound databases including visualization of chemical space, scaffold content, and analysis of chemical diversity. The user's input is a file with SMILES, database names, and compound IDs. PUMA computes molecular properties of pharmaceutical relevance, Murcko scaffolds, and diversity analysis. The user can interactively navigate through the graphs and export image files and the raw data of the diversity calculations. The platform links two public online resources: Consensus Diversity Plots for the assessment of global diversity and Activity Landscape Plotter to analyze structure-activity relationships. Herein, we describe the functionalities of PUMA and exemplify its use through the analysis of compound databases of general interest. PUMA is freely accessible at the authors web-site https://www.difacquim.com/d-tools/ .
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Affiliation(s)
- Mariana González-Medina
- School of Chemistry, Department of Pharmacy, Universidad Nacional Autónoma de México , Avenida Universidad 3000, Mexico City 04510, Mexico
| | - José L Medina-Franco
- School of Chemistry, Department of Pharmacy, Universidad Nacional Autónoma de México , Avenida Universidad 3000, Mexico City 04510, Mexico
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10
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Naveja JJ, Medina-Franco JL. ChemMaps: Towards an approach for visualizing the chemical space based on adaptive satellite compounds. F1000Res 2017; 6. [PMID: 28794856 PMCID: PMC5538041 DOI: 10.12688/f1000research.12095.2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/03/2017] [Indexed: 01/22/2023] Open
Abstract
We present a novel approach called ChemMaps for visualizing chemical space based on the similarity matrix of compound datasets generated with molecular fingerprints’ similarity. The method uses a ‘satellites’ approach, where satellites are, in principle, molecules whose similarity to the rest of the molecules in the database provides sufficient information for generating a visualization of the chemical space. Such an approach could help make chemical space visualizations more efficient. We hereby describe a proof-of-principle application of the method to various databases that have different diversity measures. Unsurprisingly, we found the method works better with databases that have low 2D diversity. 3D diversity played a secondary role, although it seems to be more relevant as 2D diversity increases. For less diverse datasets, taking as few as 25% satellites seems to be sufficient for a fair depiction of the chemical space. We propose to iteratively increase the satellites number by a factor of 5% relative to the whole database, and stop when the new and the prior chemical space correlate highly. This Research Note represents a first exploratory step, prior to the full application of this method for several datasets.
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Affiliation(s)
- J Jesús Naveja
- Department of Pharmacy, School of Chemistry, Universidad Nacional Autónoma de México, Mexico City, 04510, Mexico.,PECEM, Faculty of Medicine, Universidad Nacional Autónoma de México, Mexico City, 04510, Mexico
| | - José L Medina-Franco
- Department of Pharmacy, School of Chemistry, Universidad Nacional Autónoma de México, Mexico City, 04510, Mexico
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11
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Molecular Modeling and Chemoinformatics to Advance the Development of Modulators of Epigenetic Targets: A Focus on DNA Methyltransferases. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2016; 105:1-26. [PMID: 27567482 DOI: 10.1016/bs.apcsb.2016.05.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In light of the emerging field of Epi-informatics, ie, computational methods applied to epigenetic research, molecular docking, and dynamics, pharmacophore and activity landscape modeling and QSAR play a key role in the development of modulators of DNA methyltransferases (DNMTs), one of the major epigenetic target families. The increased chemical information available for modulators of DNMTs has opened up the avenue to explore the epigenetic relevant chemical space (ERCS). Herein, we discuss recent progress on the identification and development of inhibitors of DNMTs as potential epi-drugs and epi-probes that have been driven by molecular modeling and chemoinformatics methods. We also survey advances on the elucidation of their structure-activity relationships and exploration of ERCS. Finally, it is illustrated how computational approaches can be applied to identify modulators of DNMTs in food chemicals.
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12
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Choudhury C, Deva Priyakumar U, Narahari Sastry G. Structural and Functional Diversities of the Hexadecahydro-1H-cyclopenta[a]phenanthrene Framework, a Ubiquitous Scaffold in Steroidal Hormones. Mol Inform 2016; 35:145-57. [DOI: 10.1002/minf.201600005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 01/18/2016] [Indexed: 12/16/2022]
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13
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Grygorenko OO, Babenko P, Volochnyuk DM, Raievskyi O, Komarov IV. Following Ramachandran: exit vector plots (EVP) as a tool to navigate chemical space covered by 3D bifunctional scaffolds. The case of cycloalkanes. RSC Adv 2016. [DOI: 10.1039/c5ra19958a] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
An approach to analysis and visualization of chemical space covered by disubstituted scaffolds, which is based on exit vector plots (EVP), is used for analysis of cycloalkane. Four clearly defined regions (α, β, γ and δ) are found in their EVP.
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Affiliation(s)
| | - Pavlo Babenko
- Taras Shevchenko National University of Kyiv
- Kyiv 01601
- Ukraine
| | - Dmitry M. Volochnyuk
- Institute of Organic Chemistry National Academy of Sciences of Ukraine
- Kyiv 02094
- Ukraine
| | - Oleksii Raievskyi
- Institute of Molecular Biology and Genetics National Academy of Sciences of Ukraine
- Kyiv 03680
- Ukraine
- Life Chemicals
- Life Chemicals Group
| | - Igor V. Komarov
- Taras Shevchenko National University of Kyiv
- Kyiv 01601
- Ukraine
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14
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Johnson AR, Carlson EE. Collision-Induced Dissociation Mass Spectrometry: A Powerful Tool for Natural Product Structure Elucidation. Anal Chem 2015; 87:10668-78. [PMID: 26132379 DOI: 10.1021/acs.analchem.5b01543] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Mass spectrometry is a powerful tool in natural product structure elucidation, but our ability to directly correlate fragmentation spectra to these structures lags far behind similar efforts in peptide sequencing and proteomics. Often, manual data interpretation is required and our knowledge of the expected fragmentation patterns for many scaffolds is limited, further complicating analysis. Here, we summarize advances in natural product structure elucidation based upon the application of collision induced dissociation fragmentation mechanisms.
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Affiliation(s)
- Andrew R Johnson
- Department of Chemistry, Indiana University , 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Erin E Carlson
- Department of Chemistry, Indiana University , 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States.,Department of Molecular and Cellular Biochemistry, Indiana University , 212 South Hawthorne Drive, Bloomington, Indiana 47405, United States
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15
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Osolodkin DI, Radchenko EV, Orlov AA, Voronkov AE, Palyulin VA, Zefirov NS. Progress in visual representations of chemical space. Expert Opin Drug Discov 2015; 10:959-73. [DOI: 10.1517/17460441.2015.1060216] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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16
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Fey N. Lost in chemical space? Maps to support organometallic catalysis. Chem Cent J 2015; 9:38. [PMID: 26113874 PMCID: PMC4480443 DOI: 10.1186/s13065-015-0104-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 05/08/2015] [Indexed: 01/08/2023] Open
Abstract
Descriptors calculated from molecular structures have been used to map different areas of chemical space. A number of applications for such maps can be identified, ranging from the fine-tuning and optimisation of catalytic activity and compound properties to virtual screening of novel compounds, as well as the exhaustive exploration of large areas of chemical space by automated combinatorial building and evaluation. This review focuses on organometallic catalysis, but also touches on other areas where similar approaches have been used, with a view to assessing the extent to which chemical space has been explored. Cartoon representation of a chemical space map. ![]()
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Affiliation(s)
- Natalie Fey
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS UK
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17
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Barreiro EM, Boltukhina EV, White AJP, Hii KK(M. Atropisomeric [(diphosphine)Au2 Cl2 ] complexes and their catalytic activity towards asymmetric cycloisomerisation of 1,6-enynes. Chemistry 2015; 21:2686-90. [PMID: 25504519 PMCID: PMC4524423 DOI: 10.1002/chem.201404496] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Indexed: 11/22/2022]
Abstract
X-ray crystal structures of two [(diphosphine)Au2 Cl2 ] complexes (in which diphosphine=P-Phos and xylyl-P-Phos; P-Phos=[2,2',6,6'-Tetramethoxy-4,4'-bis(diphenylphosphino)-3,3'-bipyridine]) were determined and compared to the reported structures of similar atropisomeric gold complexes. Correlations between the Au⋅⋅⋅Au distances and torsional angles for the biaryl series of ligands (MeOBIPHEP, SEGPhos, and P-Phos; BIPHEP=2,2'-bis(diphenylphosphino)-1,1'-biphenyl, SEGPhos=[(4,4'-bi-1,3-benzodioxole)-5,5'-diyl]bis[diphenylphosphine]) can be made; these measurements appear to be very dependent upon the phosphorous substituent. Conversely, the same effect was not observed for ligands based on the binaphthyl (BINAP) series. The catalytic activity of these complexes was subsequently assessed in the enantioselective cycloisomerisation of 1,6-enynes and revealed an over-riding electronic effect: more-electron-rich phosphines promote greater enantioselectivity. The possibility of silver acting as a (co-)catalyst was ruled out in these reactions.
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Affiliation(s)
- Elena M Barreiro
- Department of Chemistry, Imperial College LondonExhibition Road, South Kensington, London SW7 2AZ (UK) E-mail:
| | | | - Andrew J P White
- Department of Chemistry, Imperial College LondonExhibition Road, South Kensington, London SW7 2AZ (UK) E-mail:
| | - King Kuok (Mimi) Hii
- Department of Chemistry, Imperial College LondonExhibition Road, South Kensington, London SW7 2AZ (UK) E-mail:
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18
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Gortari EFD, Medina-Franco JL. Epigenetic relevant chemical space: a chemoinformatic characterization of inhibitors of DNA methyltransferases. RSC Adv 2015. [DOI: 10.1039/c5ra19611f] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The first comprehensive exploration of the epigenetic relevant chemical space is reported in this work with a special emphasis on inhibitors of DNA methyltransferases.
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Affiliation(s)
- Eli Fernández-de Gortari
- Facultad de Química
- Departamento de Farmacia
- Universidad Nacional Autónoma de México
- México City 04510
- Mexico
| | - José L. Medina-Franco
- Facultad de Química
- Departamento de Farmacia
- Universidad Nacional Autónoma de México
- México City 04510
- Mexico
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19
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Ward SE, Beswick P. What does the aromatic ring number mean for drug design? Expert Opin Drug Discov 2014; 9:995-1003. [DOI: 10.1517/17460441.2014.932346] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Simon E Ward
- University of Sussex, Translational Drug Discovery Group,
Brighton, East Sussex, BN1 9QJ, UK
| | - Paul Beswick
- University of Sussex, Translational Drug Discovery Group,
Brighton, East Sussex, BN1 9QJ, UK
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20
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Medina-Franco JL, Aguayo-Ortiz R. Progress in the Visualization and Mining of Chemical and Target Spaces. Mol Inform 2013; 32:942-53. [DOI: 10.1002/minf.201300041] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Accepted: 05/06/2013] [Indexed: 01/15/2023]
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21
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Kirchmair J, Howlett A, Peironcely JE, Murrell DS, Williamson MJ, Adams SE, Hankemeier T, van Buren L, Duchateau G, Klaffke W, Glen RC. How Do Metabolites Differ from Their Parent Molecules and How Are They Excreted? J Chem Inf Model 2013; 53:354-67. [DOI: 10.1021/ci300487z] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Johannes Kirchmair
- Unilever Centre for Molecular
Sciences Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United
Kingdom
| | - Andrew Howlett
- Unilever Centre for Molecular
Sciences Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United
Kingdom
| | - Julio E. Peironcely
- TNO Research Group Quality & Safety, P.O. Box 360, 3700 AJ Zeist, The Netherlands
- Leiden/Amsterdam
Center for Drug
Research, Leiden University, Einsteinweg,
2333 CC Leiden, The Netherlands
- Netherlands Metabolomics Centre, Einsteinweg, 2333 CL Leiden, The Netherlands
| | - Daniel S. Murrell
- Unilever Centre for Molecular
Sciences Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United
Kingdom
| | - Mark J. Williamson
- Unilever Centre for Molecular
Sciences Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United
Kingdom
| | - Samuel E. Adams
- Unilever Centre for Molecular
Sciences Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United
Kingdom
| | - Thomas Hankemeier
- Leiden/Amsterdam
Center for Drug
Research, Leiden University, Einsteinweg,
2333 CC Leiden, The Netherlands
- Netherlands Metabolomics Centre, Einsteinweg, 2333 CL Leiden, The Netherlands
| | - Leo van Buren
- Unilever Research & Development, Olivier van Noortlaan, 3133 AT Vlaardingen, The Netherlands
| | - Guus Duchateau
- Unilever Research & Development, Olivier van Noortlaan, 3133 AT Vlaardingen, The Netherlands
| | - Werner Klaffke
- Unilever Research & Development, Olivier van Noortlaan, 3133 AT Vlaardingen, The Netherlands
| | - Robert C. Glen
- Unilever Centre for Molecular
Sciences Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United
Kingdom
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22
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Medina-Franco JL, Martínez-Mayorga K, Peppard TL, Del Rio A. Chemoinformatic analysis of GRAS (Generally Recognized as Safe) flavor chemicals and natural products. PLoS One 2012; 7:e50798. [PMID: 23226386 PMCID: PMC3511266 DOI: 10.1371/journal.pone.0050798] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Accepted: 10/24/2012] [Indexed: 12/15/2022] Open
Abstract
Food materials designated as "Generally Recognized as Safe" (GRAS) are attracting the attention of researchers in their attempts to systematically identify compounds with putative health-related benefits. In particular, there is currently a great deal of interest in exploring possible secondary benefits of flavor ingredients, such as those relating to health and wellness. One step in this direction is the comprehensive characterization of the chemical structures contained in databases of flavoring substances. Herein, we report a comprehensive analysis of the recently updated FEMA GRAS list of flavoring substances (discrete chemical entities only). Databases of natural products, approved drugs and a large set of commercial molecules were used as references. Remarkably, natural products continue to be an important source of bioactive compounds for drug discovery and nutraceutical purposes. The comparison of five collections of compounds of interest was performed using molecular properties, rings, atom counts and structural fingerprints. It was found that the molecular size of the GRAS flavoring substances is, in general, smaller cf. members of the other databases analyzed. The lipophilicity profile of the GRAS database, a key property to predict human bioavailability, is similar to approved drugs. Several GRAS chemicals overlap to a broad region of the property space occupied by drugs. The GRAS list analyzed in this work has high structural diversity, comparable to approved drugs, natural products and libraries of screening compounds. This study represents one step towards the use of the distinctive features of the flavoring chemicals contained in the GRAS list and natural products to systematically search for compounds with potential health-related benefits.
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Affiliation(s)
- José L Medina-Franco
- Torrey Pines Institute for Molecular Studies, Port St. Lucie, Florida, United States of America.
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