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Juárez-Mercado KE, Avellaneda-Tamayo JF, Villegas-Quintero H, Chávez-Hernández AL, López-López CD, Medina-Franco JL. Food Chemicals and Epigenetic Targets: An Epi Food Chemical Database. ACS OMEGA 2024; 9:25322-25331. [PMID: 38882162 PMCID: PMC11170626 DOI: 10.1021/acsomega.4c03321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Revised: 05/09/2024] [Accepted: 05/14/2024] [Indexed: 06/18/2024]
Abstract
There is increasing awareness of epigenetics's importance in understanding disease etiologies and developing novel therapeutics. An increasing number of publications in the past few years reflect the renewed interest in epigenetic processes and their relationship with food chemicals. However, there needs to be a recent study that accounts for the most recent advances in the area by associating the chemical structures of food and natural product components with their biological activity. Here, we analyze the status of food chemicals and their intersection with natural products in epigenetic research. Using chemoinformatics tools, we compared quantitatively the chemical contents, structural diversity, and coverage in the chemical space of food chemicals with reported epigenetic activity. As part of this work, we built and curated a compound database of food and natural product chemicals annotated with structural information, an epigenetic target activity profile, and the main source of the food chemical or natural product, among other relevant features. The compounds are cross-linked with identifiers from other major public databases such as FooDB and the collection of open natural products, COCONUT. The compound database, the "Epi Food Chemical Database", is accessible in HTML and CSV formats at https://github.com/DIFACQUIM/Epi_food_Chemical_Database.
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Affiliation(s)
- K Eurídice Juárez-Mercado
- DIFACQUIM Research Group. Department of Pharmacy, School of Chemistry, Universidad Nacional Autónoma de México, 04510 Ciudad de México, Mexico
| | - Juan F Avellaneda-Tamayo
- DIFACQUIM Research Group. Department of Pharmacy, School of Chemistry, Universidad Nacional Autónoma de México, 04510 Ciudad de México, Mexico
| | - Hassan Villegas-Quintero
- DIFACQUIM Research Group. Department of Pharmacy, School of Chemistry, Universidad Nacional Autónoma de México, 04510 Ciudad de México, Mexico
| | - Ana L Chávez-Hernández
- DIFACQUIM Research Group. Department of Pharmacy, School of Chemistry, Universidad Nacional Autónoma de México, 04510 Ciudad de México, Mexico
| | | | - José L Medina-Franco
- DIFACQUIM Research Group. Department of Pharmacy, School of Chemistry, Universidad Nacional Autónoma de México, 04510 Ciudad de México, Mexico
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2
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Martinez-Mayorga K, Rosas-Jiménez JG, Gonzalez-Ponce K, López-López E, Neme A, Medina-Franco JL. The pursuit of accurate predictive models of the bioactivity of small molecules. Chem Sci 2024; 15:1938-1952. [PMID: 38332817 PMCID: PMC10848664 DOI: 10.1039/d3sc05534e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 01/09/2024] [Indexed: 02/10/2024] Open
Abstract
Property prediction is a key interest in chemistry. For several decades there has been a continued and incremental development of mathematical models to predict properties. As more data is generated and accumulated, there seems to be more areas of opportunity to develop models with increased accuracy. The same is true if one considers the large developments in machine and deep learning models. However, along with the same areas of opportunity and development, issues and challenges remain and, with more data, new challenges emerge such as the quality and quantity and reliability of the data, and model reproducibility. Herein, we discuss the status of the accuracy of predictive models and present the authors' perspective of the direction of the field, emphasizing on good practices. We focus on predictive models of bioactive properties of small molecules relevant for drug discovery, agrochemical, food chemistry, natural product research, and related fields.
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Affiliation(s)
- Karina Martinez-Mayorga
- Institute of Chemistry, Merida Unit, National Autonomous University of Mexico Merida-Tetiz Highway, Km. 4.5 Ucu Yucatan Mexico
- Institute for Applied Mathematics and Systems, Merida Research Unit, National Autonomous University of Mexico Sierra Papacal Merida Yucatan Mexico
| | - José G Rosas-Jiménez
- Department of Theoretical Biophysics, IMPRS on Cellular Biophysics Max-von-Laue Strasse 3 Frankfurt am Main 60438 Germany
| | - Karla Gonzalez-Ponce
- Institute of Chemistry, Merida Unit, National Autonomous University of Mexico Merida-Tetiz Highway, Km. 4.5 Ucu Yucatan Mexico
| | - Edgar López-López
- Department of Chemistry and Graduate Program in Pharmacology, Center for Research and Advanced Studies of the National Polytechnic Institute Mexico City 07000 Mexico
- DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry National Autonomous University of Mexico Mexico City 04510 Mexico
| | - Antonio Neme
- Institute for Applied Mathematics and Systems, Merida Research Unit, National Autonomous University of Mexico Sierra Papacal Merida Yucatan Mexico
| | - José L Medina-Franco
- DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry National Autonomous University of Mexico Mexico City 04510 Mexico
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3
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Aldeghi M, Graff DE, Frey N, Morrone JA, Pyzer-Knapp EO, Jordan KE, Coley CW. Roughness of Molecular Property Landscapes and Its Impact on Modellability. J Chem Inf Model 2022; 62:4660-4671. [DOI: 10.1021/acs.jcim.2c00903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Matteo Aldeghi
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - David E. Graff
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Nathan Frey
- Lincoln Laboratory, Massachusetts Institute of Technology, Lexington, Massachusetts 02421, United States
| | - Joseph A. Morrone
- IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, United States
| | | | - Kirk E. Jordan
- IBM Thomas J. Watson Research Center, Cambridge, Massachusetts 02142, United States
| | - Connor W. Coley
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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Colin-Lozano B, Torres-Gomez H, Hidalgo-Figueroa S, Chávez-Silva F, Estrada-Soto S, Almanza-Pérez JC, Navarrete-Vazquez G. Synthesis, In Vitro, In Vivo and In Silico Antidiabetic Bioassays of 4-Nitro(thio)phenoxyisobutyric Acids Acting as Unexpected PPARγ Modulators: An In Combo Study. Pharmaceuticals (Basel) 2022; 15:ph15010102. [PMID: 35056159 PMCID: PMC8779174 DOI: 10.3390/ph15010102] [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] [Received: 01/04/2022] [Revised: 01/10/2022] [Accepted: 01/13/2022] [Indexed: 01/21/2023] Open
Abstract
Four isobutyric acids (two nitro and two acetamido derivatives) were prepared in two steps and characterized using spectral analysis. The mRNA concentrations of PPARγ and GLUT-4 (two proteins documented as key diabetes targets) were increased by 3T3-L1 adipocytes treated with compounds 1–4, but an absence of in vitro expression of PPARα was observed. Docking and molecular dynamics studies revealed the plausible interaction between the synthesized compounds and PPARγ. In vivo studies established that compounds 1–4 have antihyperglycemic modes of action associated with insulin sensitization. Nitrocompound 2 was the most promising of the series, being orally active, and one of multiple modes of action could be selective PPARγ modulation due to its extra anchoring with Gln-286. In conclusion, we demonstrated that nitrocompound 2 showed strong in vitro and in vivo effects and can be considered as an experimental antidiabetic candidate.
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Affiliation(s)
- Blanca Colin-Lozano
- Facultad de Farmacia, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos 62209, Mexico; (B.C.-L.); (H.T.-G.); (S.H.-F.); (F.C.-S.); (S.E.-S.)
- Facultad de Ciencias Químicas, Benemérita Universidad Autónoma de Puebla, Puebla 72000, Mexico
| | - Héctor Torres-Gomez
- Facultad de Farmacia, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos 62209, Mexico; (B.C.-L.); (H.T.-G.); (S.H.-F.); (F.C.-S.); (S.E.-S.)
- Leibniz Institute for Natural Products and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Sergio Hidalgo-Figueroa
- Facultad de Farmacia, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos 62209, Mexico; (B.C.-L.); (H.T.-G.); (S.H.-F.); (F.C.-S.); (S.E.-S.)
- CONACyT, Instituto Potosino de Investigación Científica y Tecnológica, San Luis Potosi 78216, Mexico
| | - Fabiola Chávez-Silva
- Facultad de Farmacia, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos 62209, Mexico; (B.C.-L.); (H.T.-G.); (S.H.-F.); (F.C.-S.); (S.E.-S.)
| | - Samuel Estrada-Soto
- Facultad de Farmacia, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos 62209, Mexico; (B.C.-L.); (H.T.-G.); (S.H.-F.); (F.C.-S.); (S.E.-S.)
| | - Julio Cesar Almanza-Pérez
- Laboratorio de Farmacología, Departamento de Ciencias de la Salud, Universidad Autónoma Metropolitana Iztapalapa, Mexico City 09340, Mexico;
| | - Gabriel Navarrete-Vazquez
- Facultad de Farmacia, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos 62209, Mexico; (B.C.-L.); (H.T.-G.); (S.H.-F.); (F.C.-S.); (S.E.-S.)
- Correspondence: ; Tel.: +52-777-329-7089 (ext. 2322)
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López-López E, Cerda-García-Rojas CM, Medina-Franco JL. Tubulin Inhibitors: A Chemoinformatic Analysis Using Cell-Based Data. Molecules 2021; 26:2483. [PMID: 33923169 PMCID: PMC8123128 DOI: 10.3390/molecules26092483] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 04/18/2021] [Accepted: 04/20/2021] [Indexed: 12/14/2022] Open
Abstract
Inhibiting the tubulin-microtubules (Tub-Mts) system is a classic and rational approach for treating different types of cancers. A large amount of data on inhibitors in the clinic supports Tub-Mts as a validated target. However, most of the inhibitors reported thus far have been developed around common chemical scaffolds covering a narrow region of the chemical space with limited innovation. This manuscript aims to discuss the first activity landscape and scaffold content analysis of an assembled and curated cell-based database of 851 Tub-Mts inhibitors with reported activity against five cancer cell lines and the Tub-Mts system. The structure-bioactivity relationships of the Tub-Mts system inhibitors were further explored using constellations plots. This recently developed methodology enables the rapid but quantitative assessment of analog series enriched with active compounds. The constellations plots identified promising analog series with high average biological activity that could be the starting points of new and more potent Tub-Mts inhibitors.
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Affiliation(s)
- Edgar López-López
- Departamento de Química y Programa de Posgrado en Farmacología, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Apartado 14-740, Mexico City 07000, Mexico;
- DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Carlos M. Cerda-García-Rojas
- Departamento de Química y Programa de Posgrado en Farmacología, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Apartado 14-740, Mexico City 07000, Mexico;
| | - José L. Medina-Franco
- DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
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Maggiora G, Medina-Franco JL, Iqbal J, Vogt M, Bajorath J. From Qualitative to Quantitative Analysis of Activity and Property Landscapes. J Chem Inf Model 2020; 60:5873-5880. [PMID: 33205984 DOI: 10.1021/acs.jcim.0c01249] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Activity or, more generally, property landscapes (PLs) have been considered as an attractive way to visualize and explore structure-property relationships (SPRs) contained in large data sets of chemical compounds. For graphical analysis, three-dimensional representations reminiscent of natural landscapes are particularly intuitive. So far, the use of such landscape models has essentially been confined to qualitative assessment. We describe recent efforts to analyze PLs in a more quantitative manner, which make it possible to calculate topographical similarity values for comparison of landscape models as a measure of relative SPR information content.
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Affiliation(s)
- Gerald Maggiora
- University of Arizona BIO5 Institute, 1657 East Helen Street, Tucson, Arizona 85721-0240, United States
| | - José L Medina-Franco
- Department of Pharmacy, School of Chemistry, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Javed Iqbal
- Department of Life Science Informatics, B-IT LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Endenicher Allee 19c, Bonn D-53115, Germany
| | - Martin Vogt
- Department of Life Science Informatics, B-IT LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Endenicher Allee 19c, Bonn D-53115, Germany
| | - Jürgen Bajorath
- Department of Life Science Informatics, B-IT LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Endenicher Allee 19c, Bonn D-53115, Germany
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7
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Iqbal J, Vogt M, Bajorath J. Quantitative Comparison of Three-Dimensional Activity Landscapes of Compound Data Sets Based upon Topological Features. ACS OMEGA 2020; 5:24111-24117. [PMID: 32984733 PMCID: PMC7513547 DOI: 10.1021/acsomega.0c03659] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 08/27/2020] [Indexed: 05/07/2023]
Abstract
Visualization of structure-activity relationships (SARs) in compound data sets substantially contributes to their systematic analysis. For SAR visualization, different types of activity landscape (AL) representations have been introduced. Three-dimensional (3D) AL models in which an activity hypersurface is constructed in chemical space are particularly intuitive because these 3D ALs are reminiscent of "true" (geographical) landscapes. Accordingly, the topologies of 3D AL representations can be immediately associated with different SAR characteristics of compound data sets. However, the comparison of 3D ALs has thus far been confined to visual inspection and qualitative analysis. We have focused on image analysis as a possible approach to facilitate a quantitative comparison of 3D ALs, which would further increase their utility for SAR exploration. Herein, we introduce a new computational methodology for quantifying topological relationships between 3D ALs. Images of color-coded 3D ALs were converted into top-down views of these ALs. From transformed images, different categories of shape features were systematically extracted, and multilevel shape correspondence was determined as a measure of AL similarity. This made it possible to differentiate between 3D ALs in quantitative terms.
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Affiliation(s)
- Javed Iqbal
- Department of Life Science
Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal
Chemistry, Rheinische Friedrich-Wilhelms-Universität, Endenicher Allee 19c, D-53115 Bonn, Germany
| | - Martin Vogt
- Department of Life Science
Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal
Chemistry, Rheinische Friedrich-Wilhelms-Universität, Endenicher Allee 19c, D-53115 Bonn, Germany
| | - Jürgen Bajorath
- Department of Life Science
Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal
Chemistry, Rheinische Friedrich-Wilhelms-Universität, Endenicher Allee 19c, D-53115 Bonn, Germany
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8
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Iqbal J, Vogt M, Bajorath J. Computational Method for Quantitative Comparison of Activity Landscapes on the Basis of Image Data. Molecules 2020; 25:E3952. [PMID: 32872506 PMCID: PMC7504767 DOI: 10.3390/molecules25173952] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 08/21/2020] [Accepted: 08/27/2020] [Indexed: 01/31/2023] Open
Abstract
Activity landscape (AL) models are used for visualizing and interpreting structure-activity relationships (SARs) in compound datasets. Therefore, ALs are designed to present chemical similarity and compound potency information in context. Different two- or three-dimensional (2D or 3D) AL representations have been introduced. For SAR analysis, 3D AL models are particularly intuitive. In these models, an interpolated potency surface is added as a third dimension to a 2D projection of chemical space. Accordingly, AL topology can be associated with characteristic SAR features. Going beyond visualization and a qualitative assessment of SARs, it would be very helpful to compare 3D ALs of different datasets in more quantitative terms. However, quantitative AL analysis is still in its infancy. Recently, it has been shown that 3D AL models with pre-defined topologies can be correctly classified using machine learning. Classification was facilitated on the basis of AL image feature representations learned with convolutional neural networks. Therefore, we have further investigated image analysis for quantitative comparison of 3D ALs and devised an approach to determine (dis)similarity relationships for ALs representing different compound datasets. Herein, we report this approach and demonstrate proof-of-principle. The methodology makes it possible to computationally compare 3D ALs and quantify topological differences reflecting varying SAR information content. For SAR exploration in drug design, this adds a quantitative measure of AL (dis)similarity to graphical analysis.
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Affiliation(s)
- Javed Iqbal
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Endenicher Allee 19c, D-53115 Bonn, Germany
| | - Martin Vogt
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Endenicher Allee 19c, D-53115 Bonn, Germany
| | - Jürgen Bajorath
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Endenicher Allee 19c, D-53115 Bonn, Germany
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Abstract
Abstract
The prediction of toxicological endpoints has gained broad acceptance; it is widely applied in early stages of drug discovery as well as for impurities obtained in the production of generic or equivalent products. In this work, we describe methodologies for the prediction of toxicological endpoints compounds, with a particular focus on secondary metabolites. Case studies include toxicity prediction of natural compound databases with anti-diabetic, anti-malaria and anti-HIV properties.
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Cheminformatics Explorations of Natural Products. PROGRESS IN THE CHEMISTRY OF ORGANIC NATURAL PRODUCTS 2019; 110:1-35. [PMID: 31621009 DOI: 10.1007/978-3-030-14632-0_1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The chemistry of natural products is fascinating and has continuously attracted the attention of the scientific community for many reasons including, but not limited to, biosynthesis pathways, chemical diversity, the source of bioactive compounds and their marked impact on drug discovery. There is a broad range of experimental and computational techniques (molecular modeling and cheminformatics) that have evolved over the years and have assisted the investigation of natural products. Herein, we discuss cheminformatics strategies to explore the chemistry and applications of natural products. Since the potential synergisms between cheminformatics and natural products are vast, we will focus on three major aspects: (1) exploration of the chemical space of natural products to identify bioactive compounds, with emphasis on drug discovery; (2) assessment of the toxicity profile of natural products; and (3) diversity analysis of natural product collections and the design of chemical collections inspired by natural sources.
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Saldívar-González FI, Pilón-Jiménez BA, Medina-Franco JL. Chemical space of naturally occurring compounds. PHYSICAL SCIENCES REVIEWS 2019. [DOI: 10.1515/psr-2018-0103] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
AbstractThe chemical space of naturally occurring compounds is vast and diverse. Other than biologics, naturally occurring small molecules include a large variety of compounds covering natural products from different sources such as plant, marine, and fungi, to name a few, and several food chemicals. The systematic exploration of the chemical space of naturally occurring compounds have significant implications in many areas of research including but not limited to drug discovery, nutrition, bio- and chemical diversity analysis. The exploration of the coverage and diversity of the chemical space of compound databases can be carried out in different ways. The approach will largely depend on the criteria to define the chemical space that is commonly selected based on the goals of the study. This chapter discusses major compound databases of natural products and cheminformatics strategies that have been used to characterize the chemical space of natural products. Recent exemplary studies of the chemical space of natural products from different sources and their relationships with other compounds are also discussed. We also present novel chemical descriptors and data mining approaches that are emerging to characterize the chemical space of naturally occurring compounds.
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12
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Miyao T, Funatsu K, Bajorath J. Three-Dimensional Activity Landscape Models of Different Design and Their Application to Compound Mapping and Potency Prediction. J Chem Inf Model 2018; 59:993-1004. [DOI: 10.1021/acs.jcim.8b00661] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Tomoyuki Miyao
- Data Science Center and Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
| | - Kimito Funatsu
- Data Science Center and Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Jürgen Bajorath
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Endenicher Allee 19c, D-53115 Bonn, Germany
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Abstract
INTRODUCTION Activity landscapes (ALs) are representations and models of compound data sets annotated with a target-specific activity. In contrast to quantitative structure-activity relationship (QSAR) models, ALs aim at characterizing structure-activity relationships (SARs) on a large-scale level encompassing all active compounds for specific targets. The popularity of AL modeling has grown substantially with the public availability of large activity-annotated compound data sets. AL modeling crucially depends on molecular representations and similarity metrics used to assess structural similarity. Areas covered: The concepts of AL modeling are introduced and its basis in quantitatively assessing molecular similarity is discussed. The different types of AL modeling approaches are introduced. AL designs can broadly be divided into three categories: compound-pair based, dimensionality reduction, and network approaches. Recent developments for each of these categories are discussed focusing on the application of mathematical, statistical, and machine learning tools for AL modeling. AL modeling using chemical space networks is covered in more detail. Expert opinion: AL modeling has remained a largely descriptive approach for the analysis of SARs. Beyond mere visualization, the application of analytical tools from statistics, machine learning and network theory has aided in the sophistication of AL designs and provides a step forward in transforming ALs from descriptive to predictive tools. To this end, optimizing representations that encode activity relevant features of molecules might prove to be a crucial step.
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Affiliation(s)
- Martin Vogt
- a Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry , Rheinische Friedrich-Wilhelms-Universität , Bonn , Germany
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14
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Saldívar-González FI, Naveja JJ, Palomino-Hernández O, Medina-Franco JL. Getting SMARt in drug discovery: chemoinformatics approaches for mining structure–multiple activity relationships. RSC Adv 2017. [DOI: 10.1039/c6ra26230a] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
In light of the high relevance of polypharmacology, multi-target screening is a major trend in drug discovery.
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Affiliation(s)
- Fernanda I. Saldívar-González
- Facultad de Química
- Departamento de Farmacia
- Universidad Nacional Autónoma de México
- Avenida Universidad 3000
- Mexico City 04510
| | - J. Jesús Naveja
- Facultad de Química
- Departamento de Farmacia
- Universidad Nacional Autónoma de México
- Avenida Universidad 3000
- Mexico City 04510
| | - Oscar Palomino-Hernández
- Facultad de Química
- Departamento de Farmacia
- Universidad Nacional Autónoma de México
- Avenida Universidad 3000
- Mexico City 04510
| | - José L. Medina-Franco
- Facultad de Química
- Departamento de Farmacia
- Universidad Nacional Autónoma de México
- Avenida Universidad 3000
- Mexico City 04510
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15
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García-Sánchez MO, Cruz-Monteagudo M, Medina-Franco JL. Quantitative Structure-Epigenetic Activity Relationships. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2017. [DOI: 10.1007/978-3-319-56850-8_8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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16
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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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17
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Activity landscape analysis of novel 5$$\upalpha $$-reductase inhibitors. Mol Divers 2016; 20:771-80. [DOI: 10.1007/s11030-016-9659-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 01/12/2016] [Indexed: 01/21/2023]
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Prieto-Martínez FD, Gortari EFD, Méndez-Lucio O, Medina-Franco JL. A chemical space odyssey of inhibitors of histone deacetylases and bromodomains. RSC Adv 2016. [DOI: 10.1039/c6ra07224k] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The interest in epigenetic drug and probe discovery is growing as reflected in the large amount of structure-epigenetic activity information available.
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Affiliation(s)
| | - Eli Fernández-de Gortari
- Facultad de Química
- Departamento de Farmacia
- Universidad Nacional Autónoma de México
- Mexico City 04510
- Mexico
| | - Oscar Méndez-Lucio
- Facultad de Química
- Departamento de Farmacia
- Universidad Nacional Autónoma de México
- Mexico City 04510
- Mexico
| | - José L. Medina-Franco
- Facultad de Química
- Departamento de Farmacia
- Universidad Nacional Autónoma de México
- Mexico City 04510
- Mexico
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19
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Vite-Caritino H, Méndez-Lucio O, Reyes H, Cabrera A, Chávez D, Medina-Franco JL. Advances in the development of pyridinone derivatives as non-nucleoside reverse transcriptase inhibitors. RSC Adv 2016. [DOI: 10.1039/c5ra25722k] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Medicinal chemistry, computational design and biological screening have advanced pyridin-2(1H)-one derivatives as a promising class of non-nucleoside reverse transcriptase inhibitors for the treatment of HIV/AIDS.
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Affiliation(s)
- Hugo Vite-Caritino
- Facultad de Química
- Departamento de Farmacia
- Universidad Nacional Autónoma de México
- Mexico City 04510
- Mexico
| | - Oscar Méndez-Lucio
- Unilever Centre for Molecular Science Informatics
- Department of Chemistry
- University of Cambridge
- Cambridge CB2 1EW
- UK
| | - Héctor Reyes
- Centro de Graduados e Investigación en Química del Instituto Tecnológico de Tijuana
- Tijuana
- Mexico
| | - Alberto Cabrera
- Centro de Graduados e Investigación en Química del Instituto Tecnológico de Tijuana
- Tijuana
- Mexico
| | - Daniel Chávez
- Centro de Graduados e Investigación en Química del Instituto Tecnológico de Tijuana
- Tijuana
- Mexico
| | - José L. Medina-Franco
- Facultad de Química
- Departamento de Farmacia
- Universidad Nacional Autónoma de México
- Mexico City 04510
- Mexico
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20
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Camacho-Mendoza RL, Gutiérrez-Moreno E, Guzmán-Percástegui E, Aquino-Torres E, Cruz-Borbolla J, Rodríguez-Ávila JA, Alvarado-Rodríguez JG, Olvera-Neria O, Thangarasu P, Medina-Franco JL. Density Functional Theory and Electrochemical Studies: Structure–Efficiency Relationship on Corrosion Inhibition. J Chem Inf Model 2015; 55:2391-402. [DOI: 10.1021/acs.jcim.5b00385] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Rosa L. Camacho-Mendoza
- Área
Académica de Química, Universidad Autónoma del Estado de Hidalgo, Unidad Universitaria, km 4.5 Carretera Pachuca-Tulancingo, C.P. 42184, Pachuca-Hidalgo, México
| | - Evelin Gutiérrez-Moreno
- Área
Académica de Química, Universidad Autónoma del Estado de Hidalgo, Unidad Universitaria, km 4.5 Carretera Pachuca-Tulancingo, C.P. 42184, Pachuca-Hidalgo, México
| | - Edmundo Guzmán-Percástegui
- Área
Académica de Química, Universidad Autónoma del Estado de Hidalgo, Unidad Universitaria, km 4.5 Carretera Pachuca-Tulancingo, C.P. 42184, Pachuca-Hidalgo, México
| | - Eliazar Aquino-Torres
- Área
Académica de Química, Universidad Autónoma del Estado de Hidalgo, Unidad Universitaria, km 4.5 Carretera Pachuca-Tulancingo, C.P. 42184, Pachuca-Hidalgo, México
| | - Julián Cruz-Borbolla
- Área
Académica de Química, Universidad Autónoma del Estado de Hidalgo, Unidad Universitaria, km 4.5 Carretera Pachuca-Tulancingo, C.P. 42184, Pachuca-Hidalgo, México
| | - José A. Rodríguez-Ávila
- Área
Académica de Química, Universidad Autónoma del Estado de Hidalgo, Unidad Universitaria, km 4.5 Carretera Pachuca-Tulancingo, C.P. 42184, Pachuca-Hidalgo, México
| | - José G. Alvarado-Rodríguez
- Área
Académica de Química, Universidad Autónoma del Estado de Hidalgo, Unidad Universitaria, km 4.5 Carretera Pachuca-Tulancingo, C.P. 42184, Pachuca-Hidalgo, México
| | - Oscar Olvera-Neria
- Área
de Física Atómica Molecular Aplicada (FAMA), CBI, Universidad Autónoma Metropolitana-Azcapotzalco, Av. San Pablo 180, Col. Reynosa, Mexico City, C.P. 02200, México
| | - Pandiyan Thangarasu
- Facultad
de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, Mexico City, C.P. 04510, México
| | - José L. Medina-Franco
- Facultad
de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, Mexico City, C.P. 04510, México
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21
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Naveja JJ, Medina-Franco JL. Activity landscape sweeping: insights into the mechanism of inhibition and optimization of DNMT1 inhibitors. RSC Adv 2015. [DOI: 10.1039/c5ra12339a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Inhibitors of DNA methyltransferases have distinct structure–activity relationships as revealed by the activity landscape sweeping study discussed in this work.
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Affiliation(s)
- J. Jesús Naveja
- Facultad de Química
- Departamento de Farmacia
- Universidad Nacional Autónoma de México
- México
- México
| | - José L. Medina-Franco
- Facultad de Química
- Departamento de Farmacia
- Universidad Nacional Autónoma de México
- México
- México
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