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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, 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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3
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Dimova D, Gilberg E, Bajorath J. Identification and analysis of promiscuity cliffs formed by bioactive compounds and experimental implications. RSC Adv 2017. [DOI: 10.1039/c6ra27247a] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
For three promiscuity cliffs (enclosed), cliff compounds, their promiscuity degrees (PDs), and color-coded substitution sites are shown. Comparison of these cliffs suggests the design of a new analog to further explore promiscuity.
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Affiliation(s)
- Dilyana Dimova
- Department of Life Science Informatics
- B-IT
- LIMES Program Unit Chemical Biology and Medicinal Chemistry
- Rheinische Friedrich-Wilhelms-Universität
- D-53113 Bonn
| | - Erik Gilberg
- Department of Life Science Informatics
- B-IT
- LIMES Program Unit Chemical Biology and Medicinal Chemistry
- Rheinische Friedrich-Wilhelms-Universität
- D-53113 Bonn
| | - Jürgen Bajorath
- Department of Life Science Informatics
- B-IT
- LIMES Program Unit Chemical Biology and Medicinal Chemistry
- Rheinische Friedrich-Wilhelms-Universität
- D-53113 Bonn
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Martín-Acosta P, Feresin G, Tapia A, Estévez-Braun A. Microwave-Assisted Organocatalytic Intramolecular Knoevenagel/Hetero Diels–Alder Reaction with O-(Arylpropynyloxy)-Salicylaldehydes: Synthesis of Polycyclic Embelin Derivatives. J Org Chem 2016; 81:9738-9756. [DOI: 10.1021/acs.joc.6b01818] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Pedro Martín-Acosta
- Instituto
Universitario de Bio-Orgánica Antonio González (CIBICAN),
Departamento de Química Orgánica, Universidad de La Laguna, Avda. Astrofísico Francisco Sánchez No. 2, 38206, La Laguna, Tenerife, Spain
| | - Gabriela Feresin
- Instituto
de Biotecnología-Instituto de Ciencias Básicas, Universidad Nacional de San Juan, Av. Libertador General San Martín 1109 (O), CP 5400, San Juan, Argentina
| | - Alejandro Tapia
- Instituto
de Biotecnología-Instituto de Ciencias Básicas, Universidad Nacional de San Juan, Av. Libertador General San Martín 1109 (O), CP 5400, San Juan, Argentina
| | - Ana Estévez-Braun
- Instituto
Universitario de Bio-Orgánica Antonio González (CIBICAN),
Departamento de Química Orgánica, Universidad de La Laguna, Avda. Astrofísico Francisco Sánchez No. 2, 38206, La Laguna, Tenerife, Spain
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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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Kuyoc-Carrillo VF, Medina-Franco JL. Progress in the Analysis of Multiple Activity Profile of Screening Data Using Computational Approaches. Drug Dev Res 2014; 75:313-23. [DOI: 10.1002/ddr.21209] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Medina-Franco JL, Méndez-Lucio O, Martinez-Mayorga K. The Interplay Between Molecular Modeling and Chemoinformatics to Characterize Protein–Ligand and Protein–Protein Interactions Landscapes for Drug Discovery. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2014; 96:1-37. [DOI: 10.1016/bs.apcsb.2014.06.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Medina-Franco JL, Martinez-Mayorga K, Meurice N. Balancing novelty with confined chemical space in modern drug discovery. Expert Opin Drug Discov 2013; 9:151-65. [DOI: 10.1517/17460441.2014.872624] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Santos RG, Giulianotti MA, Houghten RA, Medina-Franco JL. Conditional probabilistic analysis for prediction of the activity landscape and relative compound activities. J Chem Inf Model 2013; 53:2613-25. [PMID: 23971977 PMCID: PMC3850180 DOI: 10.1021/ci400243e] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Structure-property relationships and structure-activity relationships play an important role in many research areas, such as medicinal chemistry and drug discovery. Such methods, however, have focused on providing post-hoc descriptions of such relationships based on known data. The ability for these descriptions to remain relevant when considering compounds of unknown activity, and thus the prediction of activity and property landscapes using existing data, remains little explored. In this study, we present a novel method of evaluating the ability of a compound comparison methodology to provide accurate information about a set of unknown compounds and also explore the ability of these predicted activity landscapes to prioritize active compounds over inactive. These methods are applied to three distinct and diverse sets of compounds, each with activity data for multiple targets, for a total of eight target-compound set pairs. Six methodologically distinct compound comparison methods were evaluated. We show that overall, all compound comparison methods provided an improvement in structure-activity relationship prediction over random and were able to prioritize compounds in a superior manner to random sampling, but the degree of success and therefore applicability varied markedly.
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Affiliation(s)
- Radleigh G. Santos
- Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Port St. Lucie, Florida 34987
| | - Marc A. Giulianotti
- Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Port St. Lucie, Florida 34987
| | - Richard A. Houghten
- Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Port St. Lucie, Florida 34987
| | - José L. Medina-Franco
- Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Port St. Lucie, Florida 34987
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van Linden OPJ, Kooistra AJ, Leurs R, de Esch IJP, de Graaf C. KLIFS: a knowledge-based structural database to navigate kinase-ligand interaction space. J Med Chem 2013; 57:249-77. [PMID: 23941661 DOI: 10.1021/jm400378w] [Citation(s) in RCA: 203] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Protein kinases regulate the majority of signal transduction pathways in cells and have become important targets for the development of designer drugs. We present a systematic analysis of kinase-ligand interactions in all regions of the catalytic cleft of all 1252 human kinase-ligand cocrystal structures present in the Protein Data Bank (PDB). The kinase-ligand interaction fingerprints and structure database (KLIFS) contains a consistent alignment of 85 kinase ligand binding site residues that enables the identification of family specific interaction features and classification of ligands according to their binding modes. We illustrate how systematic mining of kinase-ligand interaction space gives new insights into how conserved and selective kinase interaction hot spots can accommodate the large diversity of chemical scaffolds in kinase ligands. These analyses lead to an improved understanding of the structural requirements of kinase binding that will be useful in ligand discovery and design studies.
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Affiliation(s)
- Oscar P J van Linden
- Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), VU University Amsterdam , De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
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Yongye AB, Medina-Franco JL. Toward an Efficient Approach to Identify Molecular Scaffolds Possessing Selective or Promiscuous Compounds. Chem Biol Drug Des 2013; 82:367-75. [DOI: 10.1111/cbdd.12162] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Revised: 04/12/2013] [Accepted: 04/17/2013] [Indexed: 01/09/2023]
Affiliation(s)
- Austin B. Yongye
- Torrey Pines Institute for Molecular Studies; 11350 SW Village Parkway Port St. Lucie FL 34987 USA
| | - José L. Medina-Franco
- Torrey Pines Institute for Molecular Studies; 11350 SW Village Parkway Port St. Lucie FL 34987 USA
- Instituto de Química; Universidad Nacional Autónoma de México; Circuito Exterior; Ciudad Universitaria; México D.F 04510 Mexico
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12
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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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Compound promiscuity: what can we learn from current data? Drug Discov Today 2013; 18:644-50. [DOI: 10.1016/j.drudis.2013.03.002] [Citation(s) in RCA: 119] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Revised: 02/28/2013] [Accepted: 03/08/2013] [Indexed: 11/19/2022]
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Medina-Franco JL, Giulianotti MA, Welmaker GS, Houghten RA. Shifting from the single to the multitarget paradigm in drug discovery. Drug Discov Today 2013; 18:495-501. [PMID: 23340113 PMCID: PMC3642214 DOI: 10.1016/j.drudis.2013.01.008] [Citation(s) in RCA: 294] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Revised: 12/03/2012] [Accepted: 01/14/2013] [Indexed: 01/30/2023]
Abstract
Increasing evidence that several drug compounds exert their effects through interactions with multiple targets is boosting the development of research fields that challenge the data reductionism approach. In this article, we review and discuss the concepts of drug repurposing, polypharmacology, chemogenomics, phenotypic screening and high-throughput in vivo testing of mixture-based libraries in an integrated manner. These research fields offer alternatives to the current paradigm of drug discovery, from a one target-one drug model to a multiple-target approach. Furthermore, the goals of lead identification are being expanded accordingly to identify not only 'key' compounds that fit with a single-target 'lock', but also 'master key' compounds that favorably interact with multiple targets (i.e. operate a set of desired locks to gain access to the expected clinical effects).
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Affiliation(s)
- José L Medina-Franco
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, México, D.F. 04510, Mexico.
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Medina-Franco JL. Activity Cliffs: Facts or Artifacts? Chem Biol Drug Des 2013; 81:553-6. [DOI: 10.1111/cbdd.12115] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Revised: 01/17/2013] [Accepted: 01/27/2013] [Indexed: 01/12/2023]
Affiliation(s)
- José L. Medina-Franco
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior; Ciudad Universitaria; México; D.F. 04510; Mexico
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16
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Yongye AB, Medina-Franco JL. Systematic characterization of structure-activity relationships and ADMET compliance: a case study. Drug Discov Today 2013; 18:732-9. [PMID: 23583765 DOI: 10.1016/j.drudis.2013.04.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2012] [Revised: 03/18/2013] [Accepted: 04/04/2013] [Indexed: 01/29/2023]
Abstract
Traditionally, activity landscape modeling has been focused on analyzing SAR, despite the fact that lead optimization in drug discovery involves concurrent enhancements of activity and ADMET properties of leads. As a case study, we discuss the systematic analysis of activity landscapes, incorporating ADMET considerations, using a dataset of 166 compounds screened for kappa-opioid receptor activity. Pairwise MACCS/Tanimoto structure similarities, property similarities utilizing 33 ADMET descriptors and a 35-dimensional 'violation bit vector' representing drug-likeness are analyzed. We address the question about the range of ADMET property violations that arise from structural changes, subtle and significant. Pairs of compounds are identified bearing identical, comparable and significantly different drug-likeness in the three informative regions of structure-activity landscapes.
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Affiliation(s)
- Austin B Yongye
- Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Port St. Lucie, FL 34987, USA.
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17
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Méndez-Lucio O, Pérez-Villanueva J, Castillo R, Medina-Franco JL. Identifying Activity Cliff Generators of PPAR Ligands Using SAS Maps. Mol Inform 2012; 31:837-46. [DOI: 10.1002/minf.201200078] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2012] [Accepted: 10/06/2012] [Indexed: 01/27/2023]
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Medina-Franco JL. Scanning structure-activity relationships with structure-activity similarity and related maps: from consensus activity cliffs to selectivity switches. J Chem Inf Model 2012; 52:2485-93. [PMID: 22989212 DOI: 10.1021/ci300362x] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Systematic description of structure-activity relationships (SARs) of data sets and structure-property relationships (SPRs) is of paramount importance in medicinal chemistry and other research fields. To this end, structure-activity similarity (SAS) maps are one of the first tools proposed to describe SARs using the concept of activity landscape modeling. One of the major goals of the SAS maps is to identify activity cliffs defined as chemical compounds with high similar structure but unexpectedly very different biological activity. Since the first publication of the SAS maps more than ten years ago, these tools have evolved and adapted over the years to analyze various types of compound collections, including structural diverse and combinatorial sets with activity for one or multiple biological end points. The development of SAS maps has led to general concepts that are applicable to other activity landscape methods such as "consensus activity cliffs" (activity cliffs common to a series of representations or descriptors) and "selectivity switches" (structural changes that completely invert the selectivity pattern of similar compounds against two biological end points). Herein, we review the development, practical applications, limitations, and perspectives of the SAS and related maps which are intuitive and powerful informatics tools to computationally analyze SPRs.
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Affiliation(s)
- José L Medina-Franco
- Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Port St. Lucie, Florida 34987, USA.
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