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Flores-Carrillo P, Velázquez-López JM, Aguayo-Ortiz R, Hernández-Campos A, Trejo-Soto PJ, Yépez-Mulia L, Castillo R. Synthesis, antiprotozoal activity, and chemoinformatic analysis of 2-(methylthio)-1H-benzimidazole-5-carboxamide derivatives: Identification of new selective giardicidal and trichomonicidal compounds. Eur J Med Chem 2017; 137:211-220. [PMID: 28595066 DOI: 10.1016/j.ejmech.2017.05.058] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 05/26/2017] [Accepted: 05/28/2017] [Indexed: 11/17/2022]
Abstract
A series of twelve new 2-(methylthio)-1H-benzimidazole-5-carboxamide derivatives (1-12) were synthesized and their antiparasitic activity was tested in vitro against Giardia intestinalis, Trichomonas vaginalis and Entamoeba histolytica. Experimental evaluations showed IC50 values within the nanomolar range for all tested compounds, some showing higher activity than metronidazole and albendazole. A chemoinformatic study was used to compare the structure-activity relationship of the synthesized carboxamides with those of 91 previously studied benzimidazoles, and with some Nitazoxanide-N-methylbenzimidazole hybrids recently synthetized by our group. Compounds 1 and 3 were identified as prominent selective compounds against T. vaginalis and G. intestinalis, respectively, while compound 4 was found to be of broad spectrum against the three protozoans.
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Affiliation(s)
- Paulina Flores-Carrillo
- Facultad de Química, Departamento de Farmacia, Universidad Nacional Autónoma de México, México, CDMX 04510, Mexico
| | - José Miguel Velázquez-López
- Facultad de Química, Departamento de Farmacia, Universidad Nacional Autónoma de México, México, CDMX 04510, Mexico
| | - Rodrigo Aguayo-Ortiz
- Facultad de Química, Departamento de Farmacia, Universidad Nacional Autónoma de México, México, CDMX 04510, Mexico
| | - Alicia Hernández-Campos
- Facultad de Química, Departamento de Farmacia, Universidad Nacional Autónoma de México, México, CDMX 04510, Mexico
| | - Pedro Josué Trejo-Soto
- Facultad de Química, Departamento de Farmacia, Universidad Nacional Autónoma de México, México, CDMX 04510, Mexico
| | - Lilián Yépez-Mulia
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, IMSS, México, CDMX 06720, Mexico
| | - Rafael Castillo
- Facultad de Química, Departamento de Farmacia, Universidad Nacional Autónoma de México, México, CDMX 04510, Mexico.
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2
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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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3
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Pérez-Villanueva J, Méndez-Lucio O, Soria-Arteche O, Medina-Franco JL. Activity cliffs and activity cliff generators based on chemotype-related activity landscapes. Mol Divers 2015; 19:1021-35. [PMID: 26150300 DOI: 10.1007/s11030-015-9609-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 06/24/2015] [Indexed: 12/26/2022]
Abstract
Activity cliffs have large impact in drug discovery; therefore, their detection and quantification are of major importance. This work introduces the metric activity cliff enrichment factor and expands the previously reported activity cliff generator concept by adding chemotype information to representations of the activity landscape. To exemplify these concepts, three molecular databases with multiple biological activities were characterized. Compounds in each database were grouped into chemotype classes. Then, pairwise comparisons of structure similarities and activity differences were calculated for each compound and used to construct chemotype-based structure-activity similarity (SAS) maps. Different landscape distributions among four major regions of the SAS maps were observed for different subsets of molecules grouped in chemotypes. Based on this observation, the activity cliff enrichment factor was calculated to numerically detect chemotypes enriched in activity cliffs. Several chemotype classes were detected having major proportion of activity cliffs than the entire database. In addition, some chemotype classes comprising compounds with smooth structure activity relationships (SAR) were detected. Finally, the activity cliff generator concept was applied to compounds grouped in chemotypes to extract valuable SAR information.
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Affiliation(s)
- Jaime Pérez-Villanueva
- División de Ciencias Biológicas y de la Salud, Departamento de Sistemas Biológicos, Universidad Autónoma Metropolitana Unidad Xochimilco (UAM-X), 04960, Mexico, DF, Mexico.
| | - Oscar Méndez-Lucio
- Departamento de Farmacia, Facultad de Química, Universidad Nacional Autónoma de México (UNAM), 04510, Mexico, DF, Mexico.,Unilever Centre for Molecular Science Informatics Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Olivia Soria-Arteche
- División de Ciencias Biológicas y de la Salud, Departamento de Sistemas Biológicos, Universidad Autónoma Metropolitana Unidad Xochimilco (UAM-X), 04960, Mexico, DF, Mexico
| | - José L Medina-Franco
- Departamento de Farmacia, Facultad de Química, Universidad Nacional Autónoma de México (UNAM), 04510, Mexico, DF, Mexico
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4
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Méndez-Lucio O, Kooistra AJ, Graaf CD, Bender A, Medina-Franco JL. Analyzing Multitarget Activity Landscapes Using Protein–Ligand Interaction Fingerprints: Interaction Cliffs. J Chem Inf Model 2015; 55:251-62. [DOI: 10.1021/ci500721x] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Oscar Méndez-Lucio
- Centre
for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Albert J. Kooistra
- 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
| | - Chris de Graaf
- 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
| | - Andreas Bender
- Centre
for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - José L. Medina-Franco
- Facultad
de Química, Departamento de Farmacia, Universidad Nacional Autónoma de México, Avenida Universidad 3000, Mexico City 04510, Mexico
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5
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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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6
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Cruz-Monteagudo M, Medina-Franco JL, Pérez-Castillo Y, Nicolotti O, Cordeiro MND, Borges F. Activity cliffs in drug discovery: Dr Jekyll or Mr Hyde? Drug Discov Today 2014; 19:1069-80. [DOI: 10.1016/j.drudis.2014.02.003] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 01/23/2014] [Accepted: 02/10/2014] [Indexed: 10/25/2022]
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7
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Chemoinformatic characterization of activity and selectivity switches of antiprotozoal compounds. Future Med Chem 2013; 6:281-94. [PMID: 24279680 DOI: 10.4155/fmc.13.173] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Benzimidazole derivatives are promising compounds for the treatment of parasitic infections. The structure-activity relationships of 91 benzimidazoles with activity against Trichomonas vaginalis and Giardia intestinalis were analyzed using a novel activity landscape modeling approach. RESULTS We identified two prominent cases of 'activity switches' and 'selectivity switches' where two R group substitutions in the benzimidazole scaffold completely invert the activity and selectivity pattern for T. vaginalis and G. intestinalis. CONCLUSION A chemoinformatic methodology was used to rapidly identify discrete structural changes around the central scaffold that are associated with large changes in biological activity for each parasite. The structure-activity relationships for the benzimidazole derivatives is smooth for both protozoan with few but markedly important activity cliffs.
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Medina-Franco JL, Edwards BS, Pinilla C, Appel JR, Giulianotti MA, Santos RG, Yongye AB, Sklar LA, Houghten RA. Rapid scanning structure-activity relationships in combinatorial data sets: identification of activity switches. J Chem Inf Model 2013; 53:1475-85. [PMID: 23705689 DOI: 10.1021/ci400192y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
We present a general approach to describe the structure-activity relationships (SAR) of combinatorial data sets with activity for two biological endpoints with emphasis on the rapid identification of substitutions that have a large impact on activity and selectivity. The approach uses dual-activity difference (DAD) maps that represent a visual and quantitative analysis of all pairwise comparisons of one, two, or more substitutions around a molecular template. Scanning the SAR of data sets using DAD maps allows the visual and quantitative identification of activity switches defined as specific substitutions that have an opposite effect on the activity of the compounds against two targets. The approach also rapidly identifies single- and double-target R-cliffs, i.e., compounds where a single or double substitution around the central scaffold dramatically modifies the activity for one or two targets, respectively. The approach introduced in this report can be applied to any analogue series with two biological activity endpoints. To illustrate the approach, we discuss the SAR of 106 pyrrolidine bis-diketopiperazines tested against two formylpeptide receptors obtained from positional scanning deconvolution methods of mixture-based libraries.
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Affiliation(s)
- José L Medina-Franco
- Torrey Pines Institute for Molecular Studies, Port St. Lucie, Florida 34987, USA.
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9
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Hidalgo-Figueroa S, Ramírez-Espinosa JJ, Estrada-Soto S, Almanza-Pérez JC, Román-Ramos R, Alarcón-Aguilar FJ, Hernández-Rosado JV, Moreno-Díaz H, Díaz-Coutiño D, Navarrete-Vázquez G. Discovery of Thiazolidine-2,4-Dione/Biphenylcarbonitrile Hybrid as Dual PPAR α/γ Modulator with Antidiabetic Effect:In vitro, In SilicoandIn VivoApproaches. Chem Biol Drug Des 2013; 81:474-83. [DOI: 10.1111/cbdd.12102] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Revised: 12/06/2012] [Accepted: 12/10/2012] [Indexed: 12/20/2022]
Affiliation(s)
- Sergio Hidalgo-Figueroa
- Facultad de Farmacia; Universidad Autónoma del Estado de Morelos; Av. Universidad 1001; Chamilpa; Cuernavaca Mor.; 62209; México
| | - Juan J. Ramírez-Espinosa
- Facultad de Farmacia; Universidad Autónoma del Estado de Morelos; Av. Universidad 1001; Chamilpa; Cuernavaca Mor.; 62209; México
| | - Samuel Estrada-Soto
- Facultad de Farmacia; Universidad Autónoma del Estado de Morelos; Av. Universidad 1001; Chamilpa; Cuernavaca Mor.; 62209; México
| | - Julio C. Almanza-Pérez
- Laboratorio de Farmacología; Depto. Ciencias de la Salud, D.C.B.S.; Universidad Autónoma Metropolitana-Iztapalapa; Apdo.-Postal 55-535; CP 09340; México; D.F.; México
| | - Rubén Román-Ramos
- Laboratorio de Farmacología; Depto. Ciencias de la Salud, D.C.B.S.; Universidad Autónoma Metropolitana-Iztapalapa; Apdo.-Postal 55-535; CP 09340; México; D.F.; México
| | - Francisco J. Alarcón-Aguilar
- Laboratorio de Farmacología; Depto. Ciencias de la Salud, D.C.B.S.; Universidad Autónoma Metropolitana-Iztapalapa; Apdo.-Postal 55-535; CP 09340; México; D.F.; México
| | - Jesús V. Hernández-Rosado
- Posgrado en Biología Experimental, D.C.B.S.; Universidad Autónoma Metropolitana-Iztapalapa; Apdo.-Postal 55-535; CP 09340; México; D.F.; México
| | - Hermenegilda Moreno-Díaz
- Universidad del Papaloapan, Campus Tuxtepec; Circuito Central 200, Col. Parque Industrial; 68301; Tuxtepec; Oaxaca; México
| | - Daniel Díaz-Coutiño
- Universidad del Papaloapan, Campus Tuxtepec; Circuito Central 200, Col. Parque Industrial; 68301; Tuxtepec; Oaxaca; México
| | - Gabriel Navarrete-Vázquez
- Facultad de Farmacia; Universidad Autónoma del Estado de Morelos; Av. Universidad 1001; Chamilpa; Cuernavaca Mor.; 62209; México
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Pérez-Villanueva J, Méndez-Lucio O, Soria-Arteche O, Izquierdo T, Concepción Lozada M, Gloria-Greimel WA, Medina-Franco JL. Cyclic Systems Distribution Along Similarity Measures: Insights for an Application to Activity Landscape Modeling. Mol Inform 2013; 32:179-90. [DOI: 10.1002/minf.201200127] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Accepted: 12/21/2012] [Indexed: 12/12/2022]
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11
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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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12
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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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13
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Pérez-Villanueva J, Medina-Franco JL, Méndez-Lucio O, Yoo J, Soria-Arteche O, Izquierdo T, Lozada MC, Castillo R. CASE plots for the chemotype-based activity and selectivity analysis: a CASE study of cyclooxygenase inhibitors. Chem Biol Drug Des 2012; 80:752-62. [PMID: 22883137 DOI: 10.1111/cbdd.12019] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Structure-activity characterization of molecular databases plays a central role in drug discovery. However, the characterization of large databases containing structurally diverse molecules with several end-points represents a major challenge. For this purpose, the use of chemoinformatic methods plays an important role to elucidate structure-activity relationships. Herein, a general methodology, namely Chemotype Activity and Selectivity Enrichment plots, is presented. Chemotype Activity and Selectivity Enrichment plots provide graphical information concerning the activity and selectivity patterns of particular chemotypes contained in structurally diverse databases. As a case study, we analyzed a set of 658 compounds screened against cyclooxygenase-1 and cyclooxygenase-2. Chemotype Activity and Selectivity Enrichment plots analysis highlighted chemotypes enriched with active and selective molecules against cyclooxygenase-2; all this in a simple 2D graphical representation. Additionally, the most active and selective chemotypes detected in Chemotype Activity and Selectivity Enrichment plots were analyzed separately using the previously reported dual activity-difference maps. These findings indicate that Chemotype Activity and Selectivity Enrichment plots and dual activity-difference maps are complementary chemoinformatic tools to explore the structure-activity relationships of structurally diverse databases screened against two biological end-points.
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Affiliation(s)
- Jaime Pérez-Villanueva
- Departamento de Sistemas Biológicos, División de Ciencias Biológicas y de la Salud, UAM-X, México, DF 04960, Mexico.
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