1
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Lange JJ, Anelli A, Alsenz J, Kuentz M, O'Dwyer PJ, Saal W, Wyttenbach N, Griffin BT. Comparative Analysis of Chemical Descriptors by Machine Learning Reveals Atomistic Insights into Solute-Lipid Interactions. Mol Pharm 2024. [PMID: 38780534 DOI: 10.1021/acs.molpharmaceut.4c00080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
This study explores the research area of drug solubility in lipid excipients, an area persistently complex despite recent advancements in understanding and predicting solubility based on molecular structure. To this end, this research investigated novel descriptor sets, employing machine learning techniques to understand the determinants governing interactions between solutes and medium-chain triglycerides (MCTs). Quantitative structure-property relationships (QSPR) were constructed on an extended solubility data set comprising 182 experimental values of structurally diverse drug molecules, including both development and marketed drugs to extract meaningful property relationships. Four classes of molecular descriptors, ranging from traditional representations to complex geometrical descriptions, were assessed and compared in terms of their predictive accuracy and interpretability. These include two-dimensional (2D) and three-dimensional (3D) descriptors, Abraham solvation parameters, extended connectivity fingerprints (ECFPs), and the smooth overlap of atomic position (SOAP) descriptor. Through testing three distinct regularized regression algorithms alongside various preprocessing schemes, the SOAP descriptor enabled the construction of a superior performing model in terms of interpretability and accuracy. Its atom-centered characteristics allowed contributions to be estimated at the atomic level, thereby enabling the ranking of prevalent molecular motifs and their influence on drug solubility in MCTs. The performance on a separate test set demonstrated high predictive accuracy (RMSE = 0.50) for 2D and 3D, SOAP, and Abraham Solvation descriptors. The model trained on ECFP4 descriptors resulted in inferior predictive accuracy. Lastly, uncertainty estimations for each model were introduced to assess their applicability domains and provide information on where the models may extrapolate in chemical space and, thus, where more data may be necessary to refine a data-driven approach to predict solubility in MCTs. Overall, the presented approaches further enable computationally informed formulation development by introducing a novel in silico approach for rational drug development and prediction of dose loading in lipids.
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Affiliation(s)
- Justus Johann Lange
- School of Pharmacy, University College Cork, College Road, Cork T12 R229, Cork County, Ireland
| | - Andrea Anelli
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Limited, Grenzacherstrasse 124, Basel 4070, Switzerland
| | - Jochem Alsenz
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Limited, Grenzacherstrasse 124, Basel 4070, Switzerland
| | - Martin Kuentz
- Insitute of Pharma Technology, University of Applied Sciences and Arts Northwestern Switzerland, Hofackerstrasse 30, Muttenz CH-4231, Basel City, Switzerland
| | - Patrick J O'Dwyer
- School of Pharmacy, University College Cork, College Road, Cork T12 R229, Cork County, Ireland
| | - Wiebke Saal
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Limited, Grenzacherstrasse 124, Basel 4070, Switzerland
| | - Nicole Wyttenbach
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Limited, Grenzacherstrasse 124, Basel 4070, Switzerland
| | - Brendan T Griffin
- School of Pharmacy, University College Cork, College Road, Cork T12 R229, Cork County, Ireland
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2
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Sandoval C, Torrens F, Godoy K, Reyes C, Farías J. Application of Quantitative Structure-Activity Relationships in the Prediction of New Compounds with Anti-Leukemic Activity. Int J Mol Sci 2023; 24:12258. [PMID: 37569634 PMCID: PMC10418467 DOI: 10.3390/ijms241512258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 07/24/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023] Open
Abstract
Leukemia invades the bone marrow progressively and, through unknown mechanisms, outcompetes healthy hematopoiesis. Protein arginine methyltransferases 1 (PRMT1) are found in prokaryotes and eukaryotes cells. They are necessary for a number of biological processes and have been linked to several human diseases, including cancer. Small compounds that target PRMT1 have a significant impact on both functional research and clinical disease treatment. In fact, numerous PRMT1 inhibitors targeting the S-adenosyl-L-methionine binding region have been studied. Through topographical descriptors, quantitative structure-activity relationships (QSAR) were developed in order to identify the most effective PRMT1 inhibitors among 17 compounds. The model built using linear discriminant analysis allows us to accurately classify over 90% of the investigated active substances. Antileukemic activity is predicted using a multilinear regression analysis, and it can account for more than 56% of the variation. Both analyses are validated using an internal "leave some out" test. The developed model could be utilized in future preclinical experiments with novel drugs.
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Affiliation(s)
- Cristian Sandoval
- Escuela de Tecnología Médica, Facultad de Salud, Universidad Santo Tomás, Los Carreras 753, Osorno 5310431, Chile
- Departamento de Ingeniería Química, Facultad de Ingeniería y Ciencias, Universidad de La Frontera, Temuco 4811230, Chile
- Departamento de Ciencias Preclínicas, Facultad de Medicina, Universidad de La Frontera, Temuco 4811230, Chile
| | - Francisco Torrens
- Institut Universitari de Ciència Molecular, Universitat de València, 46071 València, Spain;
| | - Karina Godoy
- Nucleo Científico y Tecnológico en Biorecursos (BIOREN), Universidad de La Frontera, Temuco 4811230, Chile;
| | - Camila Reyes
- Carrera de Tecnología Médica, Facultad de Medicina, Universidad de La Frontera, Temuco 4811230, Chile;
| | - Jorge Farías
- Departamento de Ingeniería Química, Facultad de Ingeniería y Ciencias, Universidad de La Frontera, Temuco 4811230, Chile
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3
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Sandoval C, Torrens F, Godoy K, Reyes C, Farías J. Application of Quantitative Structure-Activity Relationships in the Prediction of New Compounds with Anti-Leukemic Activity. Int J Mol Sci 2023; 24:12258. [DOI: https:/doi.org/10.3390/ijms241512258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023] Open
Abstract
Leukemia invades the bone marrow progressively and, through unknown mechanisms, outcompetes healthy hematopoiesis. Protein arginine methyltransferases 1 (PRMT1) are found in prokaryotes and eukaryotes cells. They are necessary for a number of biological processes and have been linked to several human diseases, including cancer. Small compounds that target PRMT1 have a significant impact on both functional research and clinical disease treatment. In fact, numerous PRMT1 inhibitors targeting the S-adenosyl-L-methionine binding region have been studied. Through topographical descriptors, quantitative structure-activity relationships (QSAR) were developed in order to identify the most effective PRMT1 inhibitors among 17 compounds. The model built using linear discriminant analysis allows us to accurately classify over 90% of the investigated active substances. Antileukemic activity is predicted using a multilinear regression analysis, and it can account for more than 56% of the variation. Both analyses are validated using an internal “leave some out” test. The developed model could be utilized in future preclinical experiments with novel drugs.
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Affiliation(s)
- Cristian Sandoval
- Escuela de Tecnología Médica, Facultad de Salud, Universidad Santo Tomás, Los Carreras 753, Osorno 5310431, Chile
- Departamento de Ingeniería Química, Facultad de Ingeniería y Ciencias, Universidad de La Frontera, Temuco 4811230, Chile
- Departamento de Ciencias Preclínicas, Facultad de Medicina, Universidad de La Frontera, Temuco 4811230, Chile
| | - Francisco Torrens
- Institut Universitari de Ciència Molecular, Universitat de València, 46071 València, Spain
| | - Karina Godoy
- Nucleo Científico y Tecnológico en Biorecursos (BIOREN), Universidad de La Frontera, Temuco 4811230, Chile
| | - Camila Reyes
- Carrera de Tecnología Médica, Facultad de Medicina, Universidad de La Frontera, Temuco 4811230, Chile
| | - Jorge Farías
- Departamento de Ingeniería Química, Facultad de Ingeniería y Ciencias, Universidad de La Frontera, Temuco 4811230, Chile
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4
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García-García Á, de Julián-Ortiz JV, Gálvez J, Font D, Ayats C, Guna Serrano MDR, Muñoz-Collado C, Borrás R, Villalgordo JM. Similarity-Based Virtual Screening to Find Antituberculosis Agents Based on Novel Scaffolds: Design, Syntheses and Pharmacological Assays. Int J Mol Sci 2022; 23:ijms232315057. [PMID: 36499384 PMCID: PMC9737236 DOI: 10.3390/ijms232315057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 11/02/2022] [Accepted: 11/22/2022] [Indexed: 12/04/2022] Open
Abstract
A method to identify molecular scaffolds potentially active against the Mycobacterium tuberculosis complex (MTBC) is developed. A set of structurally heterogeneous agents against MTBC was used to obtain a mathematical model based on topological descriptors. This model was statistically validated through a Leave-n-Out test. It successfully discriminated between active or inactive compounds over 86% in database sets. It was also useful to select new potential antituberculosis compounds in external databases. The selection of new substituted pyrimidines, pyrimidones and triazolo[1,5-a]pyrimidines was particularly interesting because these structures could provide new scaffolds in this field. The seven selected candidates were synthesized and six of them showed activity in vitro.
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Affiliation(s)
- Ángela García-García
- Unidad de Investigación de Diseño de Fármacos y Conectividad Molecular, Departamento de Química Física, Facultad de Farmacia, Universitat de València, 46100 Burjassot, Spain
| | - Jesus Vicente de Julián-Ortiz
- Unidad de Investigación de Diseño de Fármacos y Conectividad Molecular, Departamento de Química Física, Facultad de Farmacia, Universitat de València, 46100 Burjassot, Spain
- Correspondence:
| | - Jorge Gálvez
- Unidad de Investigación de Diseño de Fármacos y Conectividad Molecular, Departamento de Química Física, Facultad de Farmacia, Universitat de València, 46100 Burjassot, Spain
| | - David Font
- Departamento de Química, Universitat de Girona, 17071 Girona, Spain
| | - Carles Ayats
- Departamento de Química, Universitat de Girona, 17071 Girona, Spain
| | - María del Remedio Guna Serrano
- Unidad de Investigación de Diseño de Fármacos y Conectividad Molecular, Departamento de Química Física, Facultad de Farmacia, Universitat de València, 46100 Burjassot, Spain
- Departamento de Microbiología, Facultad de Medicina y Odontología, Universitat de València, 46010 València, Spain
| | - Carlos Muñoz-Collado
- Departamento de Microbiología, Facultad de Medicina y Odontología, Universitat de València, 46010 València, Spain
| | - Rafael Borrás
- Departamento de Microbiología, Facultad de Medicina y Odontología, Universitat de València, 46010 València, Spain
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5
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Bueso-Bordils JI, Alemán-López PA, Martín-Algarra R, Duart MJ, Falcó A, Antón-Fos GM. Molecular Topology for the Search of New Anti-MRSA Compounds. Int J Mol Sci 2021; 22:ijms22115823. [PMID: 34072353 PMCID: PMC8199290 DOI: 10.3390/ijms22115823] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/21/2021] [Accepted: 05/26/2021] [Indexed: 01/04/2023] Open
Abstract
The variability of methicillin-resistant Staphylococcus aureus (MRSA), its rapid adaptive response against environmental changes, and its continued acquisition of antibiotic resistance determinants have made it commonplace in hospitals, where it causes the problem of multidrug resistance. In this study, we used molecular topology to develop several discriminant equations capable of classifying compounds according to their anti-MRSA activity. Topological indices were used as structural descriptors and their relationship with anti-MRSA activity was determined by applying linear discriminant analysis (LDA) on a group of quinolones and quinolone-like compounds. Four extra equations were constructed, named DFMRSA1, DFMRSA2, DFMRSA3 and DFMRSA4 (DFMRSA was built in a previous study), all with good statistical parameters, such as Fisher-Snedecor F (>68 in all cases), Wilk's lambda (<0.13 in all cases), and percentage of correct classification (>94% in all cases), which allows a reliable extrapolation prediction of antibacterial activity in any organic compound. The results obtained clearly reveal the high efficiency of combining molecular topology with LDA for the prediction of anti-MRSA activity.
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Affiliation(s)
- Jose I. Bueso-Bordils
- Departamento de Farmacia, Universidad Cardenal Herrera-CEU, CEU Universities C/Ramón y Cajal s/n, 46115 Alfara del Patriarca, Valencia, Spain; (P.A.A.-L.); (R.M.-A.); (M.J.D.); (G.M.A.-F.)
- Correspondence: ; Tel.: +34-96-1369000
| | - Pedro A. Alemán-López
- Departamento de Farmacia, Universidad Cardenal Herrera-CEU, CEU Universities C/Ramón y Cajal s/n, 46115 Alfara del Patriarca, Valencia, Spain; (P.A.A.-L.); (R.M.-A.); (M.J.D.); (G.M.A.-F.)
| | - Rafael Martín-Algarra
- Departamento de Farmacia, Universidad Cardenal Herrera-CEU, CEU Universities C/Ramón y Cajal s/n, 46115 Alfara del Patriarca, Valencia, Spain; (P.A.A.-L.); (R.M.-A.); (M.J.D.); (G.M.A.-F.)
| | - Maria J. Duart
- Departamento de Farmacia, Universidad Cardenal Herrera-CEU, CEU Universities C/Ramón y Cajal s/n, 46115 Alfara del Patriarca, Valencia, Spain; (P.A.A.-L.); (R.M.-A.); (M.J.D.); (G.M.A.-F.)
| | - Antonio Falcó
- ESI International Chair@CEU-UCH, Departamento de Matemáticas, Física y Ciencias Tecnológicas, Universidad Cardenal Herrera-CEU, CEU Universities San Bartolomé 55, 46115 Alfara del Patriarca, Valencia, Spain;
| | - Gerardo M. Antón-Fos
- Departamento de Farmacia, Universidad Cardenal Herrera-CEU, CEU Universities C/Ramón y Cajal s/n, 46115 Alfara del Patriarca, Valencia, Spain; (P.A.A.-L.); (R.M.-A.); (M.J.D.); (G.M.A.-F.)
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6
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Cai Y, Zhu W, Zhao S, Dong C, Xu Z, Zhao Y. Difluorocarbene-Mediated Cascade Cyclization: The Multifunctional Role of Ruppert-Prakash Reagent. Org Lett 2021; 23:3546-3551. [PMID: 33913711 DOI: 10.1021/acs.orglett.1c00962] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A difluorocarbene-mediated cascade cyclization reaction for rapid access to gem-difluorinated 3-coumaranone derivatives was developed. The difluorocarbene acts as a bipolar CF2 building block, which enables a homologation cyclization process via sequentially reacting with the phenolate and the ester group on the same substrate. The potential application of this synthetic approach is demonstrated by a late-stage modification of diethylstilbestrol. Mechanistic studies revealed the multiple crucial roles played by the Ruppert-Prakash reagent.
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Affiliation(s)
- Yanyao Cai
- Key Laboratory of Organofluorine Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Ling-Ling Road, Shanghai 200032, China
| | - Wenjie Zhu
- Key Laboratory of Organofluorine Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Ling-Ling Road, Shanghai 200032, China
| | - Shujuan Zhao
- Key Laboratory of Organofluorine Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Ling-Ling Road, Shanghai 200032, China
| | - Chanjuan Dong
- Key Laboratory of Organofluorine Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Ling-Ling Road, Shanghai 200032, China
| | - Zhenchuang Xu
- Key Laboratory of Organofluorine Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Ling-Ling Road, Shanghai 200032, China
| | - Yanchuan Zhao
- Key Laboratory of Organofluorine Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Ling-Ling Road, Shanghai 200032, China.,Key Laboratory of Energy Regulation Materials, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Ling-Ling Road, Shanghai 200032, China
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7
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Bueso-Bordils JI, Alemán-López PA, Suay-García B, Martín-Algarra R, Duart MJ, Falcó A, Antón-Fos GM. Molecular Topology for the Discovery of New Broad-Spectrum Antibacterial Drugs. Biomolecules 2020; 10:E1343. [PMID: 32961733 PMCID: PMC7564208 DOI: 10.3390/biom10091343] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/11/2020] [Accepted: 09/17/2020] [Indexed: 01/06/2023] Open
Abstract
In this study, molecular topology was used to develop several discriminant equations capable of classifying compounds according to their antibacterial activity. Topological indices were used as structural descriptors and their relation to antibacterial activity was determined by applying linear discriminant analysis (LDA) on a group of quinolones and quinolone-like compounds. Four equations were constructed, named DF1, DF2, DF3, and DF4, all with good statistical parameters such as Fisher-Snedecor's F (over 25 in all cases), Wilk's lambda (below 0.36 in all cases) and percentage of correct classification (over 80% in all cases), which allows a reliable extrapolation prediction of antibacterial activity in any organic compound. From the four discriminant functions, it can be extracted that the presence of sp3 carbons, ramifications, and secondary amine groups in a molecule enhance antibacterial activity, whereas the presence of 5-member rings, sp2 carbons, and sp2 oxygens hinder it. The results obtained clearly reveal the high efficiency of combining molecular topology with LDA for the prediction of antibacterial activity.
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Affiliation(s)
- Jose I. Bueso-Bordils
- Departamento de Farmacia, Universidad Cardenal Herrera-CEU, CEU Universities C/Ramón y Cajal s/n, 46115 Alfara del Patriarca (Valencia), Spain; (P.A.A.-L.); (R.M.-A.); (M.J.D.); (G.M.A.-F.)
| | - Pedro A. Alemán-López
- Departamento de Farmacia, Universidad Cardenal Herrera-CEU, CEU Universities C/Ramón y Cajal s/n, 46115 Alfara del Patriarca (Valencia), Spain; (P.A.A.-L.); (R.M.-A.); (M.J.D.); (G.M.A.-F.)
| | - Beatriz Suay-García
- ESI International Chair@CEU-UCH, Departamento de Matemáticas, Física y Ciencias Tecnológicas, Universidad Cardenal Herrera-CEU, CEU Universities San Bartolomé 55, 46115 Alfara del Patriarca (Valencia), Spain; (B.S.-G.); (A.F.)
| | - Rafael Martín-Algarra
- Departamento de Farmacia, Universidad Cardenal Herrera-CEU, CEU Universities C/Ramón y Cajal s/n, 46115 Alfara del Patriarca (Valencia), Spain; (P.A.A.-L.); (R.M.-A.); (M.J.D.); (G.M.A.-F.)
| | - Maria J. Duart
- Departamento de Farmacia, Universidad Cardenal Herrera-CEU, CEU Universities C/Ramón y Cajal s/n, 46115 Alfara del Patriarca (Valencia), Spain; (P.A.A.-L.); (R.M.-A.); (M.J.D.); (G.M.A.-F.)
| | - Antonio Falcó
- ESI International Chair@CEU-UCH, Departamento de Matemáticas, Física y Ciencias Tecnológicas, Universidad Cardenal Herrera-CEU, CEU Universities San Bartolomé 55, 46115 Alfara del Patriarca (Valencia), Spain; (B.S.-G.); (A.F.)
| | - Gerardo M. Antón-Fos
- Departamento de Farmacia, Universidad Cardenal Herrera-CEU, CEU Universities C/Ramón y Cajal s/n, 46115 Alfara del Patriarca (Valencia), Spain; (P.A.A.-L.); (R.M.-A.); (M.J.D.); (G.M.A.-F.)
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8
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Zahrt AF, Athavale SV, Denmark SE. Quantitative Structure-Selectivity Relationships in Enantioselective Catalysis: Past, Present, and Future. Chem Rev 2020; 120:1620-1689. [PMID: 31886649 PMCID: PMC7018559 DOI: 10.1021/acs.chemrev.9b00425] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The dawn of the 21st century has brought with it a surge of research related to computer-guided approaches to catalyst design. In the past two decades, chemoinformatics, the application of informatics to solve problems in chemistry, has increasingly influenced prediction of activity and mechanistic investigations of organic reactions. The advent of advanced statistical and machine learning methods, as well as dramatic increases in computational speed and memory, has contributed to this emerging field of study. This review summarizes strategies to employ quantitative structure-selectivity relationships (QSSR) in asymmetric catalytic reactions. The coverage is structured by initially introducing the basic features of these methods. Subsequent topics are discussed according to increasing complexity of molecular representations. As the most applied subfield of QSSR in enantioselective catalysis, the application of local parametrization approaches and linear free energy relationships (LFERs) along with multivariate modeling techniques is described first. This section is followed by a description of global parametrization methods, the first of which is continuous chirality measures (CCM) because it is a single parameter derived from the global structure of a molecule. Chirality codes, global, multivariate descriptors, are then introduced followed by molecular interaction fields (MIFs), a global descriptor class that typically has the highest dimensionality. To highlight the current reach of QSSR in enantioselective transformations, a comprehensive collection of examples is presented. When combined with traditional experimental approaches, chemoinformatics holds great promise to predict new catalyst structures, rationalize mechanistic behavior, and profoundly change the way chemists discover and optimize reactions.
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Affiliation(s)
- Andrew F. Zahrt
- Roger Adams Laboratory, Department of Chemistry, University of Illinois, Urbana, IL 61801
| | - Soumitra V. Athavale
- Roger Adams Laboratory, Department of Chemistry, University of Illinois, Urbana, IL 61801
| | - Scott E. Denmark
- Roger Adams Laboratory, Department of Chemistry, University of Illinois, Urbana, IL 61801
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9
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García-Pereira I, Zanni R, Galvez-Llompart M, Galvez J, García-Domenech R. DesMol2, an Effective Tool for the Construction of Molecular Libraries and Its Application to QSAR Using Molecular Topology. Molecules 2019; 24:molecules24040736. [PMID: 30781706 PMCID: PMC6413007 DOI: 10.3390/molecules24040736] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 02/14/2019] [Accepted: 02/15/2019] [Indexed: 01/05/2023] Open
Abstract
A web application, DesMol2, which offers two main functionalities, is presented: the construction of molecular libraries and the calculation of topological indices. These functionalities are explained through a practical example of research of active molecules to the formylpeptide receptor (FPR), a receptor associated with chronic inflammation in systemic amyloidosis and Alzheimer’s disease. Starting from a data(base) of 106 dioxopiperazine pyrrolidin piperazine derivatives and their respective constant values of binding affinity to FPR, multilinear regression and discriminant analyses are performed to calculate several predictive topological-mathematical models. Next, using the DesMol2 application, a molecular library consisting of 6,120 molecules is built and performed for each predictive model. The best potential active candidates are selected and compared with results from other previous works.
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Affiliation(s)
- Inma García-Pereira
- Institute of Robotics and Information and Communication Technologies (IRTIC), University of Valencia, 46100 Valencia, Spain.
| | - Riccardo Zanni
- Molecular Topology and Drug Design Unit, Department of Physical Chemistry, University of Valencia, Avenida V.A. Estelles s/n, Burjassot, 46100 Valencia, Spain.
| | - Maria Galvez-Llompart
- Molecular Topology and Drug Design Unit, Department of Physical Chemistry, University of Valencia, Avenida V.A. Estelles s/n, Burjassot, 46100 Valencia, Spain.
- Microbiology and Plant Pathology-Unit (CSIC Associated), Department of Microbiology, Faculty of Sciences, University of Malaga, 29071 Malaga, Spain.
| | - Jorge Galvez
- Molecular Topology and Drug Design Unit, Department of Physical Chemistry, University of Valencia, Avenida V.A. Estelles s/n, Burjassot, 46100 Valencia, Spain.
| | - Ramón García-Domenech
- Molecular Topology and Drug Design Unit, Department of Physical Chemistry, University of Valencia, Avenida V.A. Estelles s/n, Burjassot, 46100 Valencia, Spain.
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10
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Sun G, Fan T, Sun X, Hao Y, Cui X, Zhao L, Ren T, Zhou Y, Zhong R, Peng Y. In Silico Prediction of O⁶-Methylguanine-DNA Methyltransferase Inhibitory Potency of Base Analogs with QSAR and Machine Learning Methods. Molecules 2018; 23:E2892. [PMID: 30404161 PMCID: PMC6278368 DOI: 10.3390/molecules23112892] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Revised: 11/04/2018] [Accepted: 11/06/2018] [Indexed: 12/24/2022] Open
Abstract
O⁶-methylguanine-DNA methyltransferase (MGMT), a unique DNA repair enzyme, can confer resistance to DNA anticancer alkylating agents that modify the O⁶-position of guanine. Thus, inhibition of MGMT activity in tumors has a great interest for cancer researchers because it can significantly improve the anticancer efficacy of such alkylating agents. In this study, we performed a quantitative structure activity relationship (QSAR) and classification study based on a total of 134 base analogs related to their ED50 values (50% inhibitory concentration) against MGMT. Molecular information of all compounds were described by quantum chemical descriptors and Dragon descriptors. Genetic algorithm (GA) and multiple linear regression (MLR) analysis were combined to develop QSAR models. Classification models were generated by seven machine-learning methods based on six types of molecular fingerprints. Performances of all developed models were assessed by internal and external validation techniques. The best QSAR model was obtained with Q²Loo = 0.83, R² = 0.87, Q²ext = 0.67, and R²ext = 0.69 based on 84 compounds. The results from QSAR studies indicated topological charge indices, polarizability, ionization potential (IP), and number of primary aromatic amines are main contributors for MGMT inhibition of base analogs. For classification studies, the accuracies of 10-fold cross-validation ranged from 0.750 to 0.885 for top ten models. The range of accuracy for the external test set ranged from 0.800 to 0.880 except for PubChem-Tree model, suggesting a satisfactory predictive ability. Three models (Ext-SVM, Ext-Tree and Graph-RF) showed high and reliable predictive accuracy for both training and external test sets. In addition, several representative substructures for characterizing MGMT inhibitors were identified by information gain and substructure frequency analysis method. Our studies might be useful for further study to design and rapidly identify potential MGMT inhibitors.
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Affiliation(s)
- Guohui Sun
- Beijing Key Laboratory of Environmental & Viral Oncology, College of Life Science & Bioengineering, Beijing University of Technology, Beijing 100124, China.
| | - Tengjiao Fan
- Beijing Key Laboratory of Environmental & Viral Oncology, College of Life Science & Bioengineering, Beijing University of Technology, Beijing 100124, China.
| | - Xiaodong Sun
- Beijing Key Laboratory of Environmental & Viral Oncology, College of Life Science & Bioengineering, Beijing University of Technology, Beijing 100124, China.
| | - Yuxing Hao
- Beijing Key Laboratory of Environmental & Viral Oncology, College of Life Science & Bioengineering, Beijing University of Technology, Beijing 100124, China.
| | - Xin Cui
- Beijing Key Laboratory of Environmental & Viral Oncology, College of Life Science & Bioengineering, Beijing University of Technology, Beijing 100124, China.
| | - Lijiao Zhao
- Beijing Key Laboratory of Environmental & Viral Oncology, College of Life Science & Bioengineering, Beijing University of Technology, Beijing 100124, China.
| | - Ting Ren
- Beijing Key Laboratory of Environmental & Viral Oncology, College of Life Science & Bioengineering, Beijing University of Technology, Beijing 100124, China.
| | - Yue Zhou
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, 2A Nanwei Road, Beijing 100050, China.
| | - Rugang Zhong
- Beijing Key Laboratory of Environmental & Viral Oncology, College of Life Science & Bioengineering, Beijing University of Technology, Beijing 100124, China.
| | - Yongzhen Peng
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment & Reuse Technology, Engineering Research Center of Beijing, Beijing University of Technology, Beijing 100124, China.
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11
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Molecular topology and QSAR multi-target analysis to boost the in silico research for fungicides in agricultural chemistry. Mol Divers 2018; 23:371-379. [PMID: 30284694 DOI: 10.1007/s11030-018-9879-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 09/25/2018] [Indexed: 01/31/2023]
Abstract
The aim of the present study is to show how molecular topology can be a powerful in silico tool for the prediction of the fungicidal activity of several diphenylamine derivatives against three fungal species (cucumber downy mildew, rice blast and cucumber gray mold). A multi-target QSAR model was developed, and two strategies were followed. First is the construction of a virtual library of molecules using DesMol2 program and a subsequent selection of potential active ones. Second is the selection of molecules from the literature on the basis of molecular scaffolds. More than 700 diphenylamine derivatives designed and other 60 fluazinam's derivatives with structural similarity higher than 80% were studied. Almost twenty percent of the molecules analyzed show potential activity against the three fungal species.
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12
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Zanni R, Garcia-Domenech R, Galvez-Llompart M, Galvez J. Alzheimer: A Decade of Drug Design. Why Molecular Topology can be an Extra Edge? Curr Neuropharmacol 2018; 16:849-864. [PMID: 29189164 PMCID: PMC6080094 DOI: 10.2174/1570159x15666171129102042] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 09/26/2017] [Accepted: 10/10/2017] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND The last decade was characterized by a growing awareness about the severity of dementia in the field of age-related and no age-related diseases and about the importance to invest resources in the research of new, effective treatments. Among the dementias, Alzheimer's plays a substantial role because of its extremely high incidence and fatality. Several pharmacological strategies have been tried but still now, Alzheimer keeps being an untreatable disease. In literature, the number of QSAR related drug design attempts about new treatments for Alzheimer is huge, but only few results can be considered noteworthy. Providing a detailed analysis of the actual situation and reporting the most notable results in the field of drug design and discovery, the current review focuses on the potential of molecular topology as a reliable tool in finding new anti-Alzheimer lead compounds. METHODS Published works on QSAR applied to the search of anti-Alzheimer's drugs during the last 10 years has been tracked. 2D and 3D-QSAR, HQSAR, topological indexes, etc. have been analyzed, as well as different mechanisms of action, such as MAO, AchE, etc. An example of topological indexes' application to the search of potential anti-Alzheimer drugs is reported. RESULTS Results show that QSAR methods during the last decade represented an excellent approach to the search of new effective drugs against Alzheimer's. In particular, QSAR based on molecular topology allows the establishment of a direct structure-property link that results in the identification of new hits and leads. CONCLUSION Molecular topology is a powerful tool for the discovery of new anti-Alzheimer drugs covering simultaneously different mechanisms of action, what may help to find a definitive cure for the disease.
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Affiliation(s)
- Riccardo Zanni
- Molecular Topology and Drug Design Unit. Department of Physical Chemistry, University of Valencia, Valencia, Spain.,Department of Microbiology, University of Malaga, Malaga, Spain
| | - Ramon Garcia-Domenech
- Molecular Topology and Drug Design Unit. Department of Physical Chemistry, University of Valencia, Valencia, Spain
| | - Maria Galvez-Llompart
- Molecular Topology and Drug Design Unit. Department of Physical Chemistry, University of Valencia, Valencia, Spain.,Department of Microbiology, University of Malaga, Malaga, Spain
| | - Jorge Galvez
- Molecular Topology and Drug Design Unit. Department of Physical Chemistry, University of Valencia, Valencia, Spain
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13
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Fan T, Sun G, Zhao L, Cui X, Zhong R. QSAR and Classification Study on Prediction of Acute Oral Toxicity of N-Nitroso Compounds. Int J Mol Sci 2018; 19:E3015. [PMID: 30282923 PMCID: PMC6213880 DOI: 10.3390/ijms19103015] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 09/29/2018] [Accepted: 09/30/2018] [Indexed: 12/30/2022] Open
Abstract
To better understand the mechanism of in vivo toxicity of N-nitroso compounds (NNCs), the toxicity data of 80 NNCs related to their rat acute oral toxicity data (50% lethal dose concentration, LD50) were used to establish quantitative structure-activity relationship (QSAR) and classification models. Quantum chemistry methods calculated descriptors and Dragon descriptors were combined to describe the molecular information of all compounds. Genetic algorithm (GA) and multiple linear regression (MLR) analyses were combined to develop QSAR models. Fingerprints and machine learning methods were used to establish classification models. The quality and predictive performance of all established models were evaluated by internal and external validation techniques. The best GA-MLR-based QSAR model containing eight molecular descriptors was obtained with Q²loo = 0.7533, R² = 0.8071, Q²ext = 0.7041 and R²ext = 0.7195. The results derived from QSAR studies showed that the acute oral toxicity of NNCs mainly depends on three factors, namely, the polarizability, the ionization potential (IP) and the presence/absence and frequency of C⁻O bond. For classification studies, the best model was obtained using the MACCS keys fingerprint combined with artificial neural network (ANN) algorithm. The classification models suggested that several representative substructures, including nitrile, hetero N nonbasic, alkylchloride and amine-containing fragments are main contributors for the high toxicity of NNCs. Overall, the developed QSAR and classification models of the rat acute oral toxicity of NNCs showed satisfying predictive abilities. The results provide an insight into the understanding of the toxicity mechanism of NNCs in vivo, which might be used for a preliminary assessment of NNCs toxicity to mammals.
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Affiliation(s)
- Tengjiao Fan
- Beijing Key Laboratory of Environmental & Viral Oncology, College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, China.
| | - Guohui Sun
- Beijing Key Laboratory of Environmental & Viral Oncology, College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, China.
| | - Lijiao Zhao
- Beijing Key Laboratory of Environmental & Viral Oncology, College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, China.
| | - Xin Cui
- Beijing Key Laboratory of Environmental & Viral Oncology, College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, China.
| | - Rugang Zhong
- Beijing Key Laboratory of Environmental & Viral Oncology, College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, China.
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14
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Lawrenson AS, Cooper DL, O'Neill PM, Berry NG. Study of the antimalarial activity of 4-aminoquinoline compounds against chloroquine-sensitive and chloroquine-resistant parasite strains. J Mol Model 2018; 24:237. [PMID: 30120591 PMCID: PMC6097041 DOI: 10.1007/s00894-018-3755-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 07/20/2018] [Indexed: 11/14/2022]
Abstract
This study is concerned with identifying features of 4-aminoquinoline scaffolds that can help pinpoint characteristics that enhance activity against chloroquine-resistant parasites. Statistically valid predictive models are reported for a series of 4-aminoquinoline analogues that are active against chloroquine-sensitive (NF54) and chloroquine-resistant (K1) strains of Plasmodium falciparum. Quantitative structure activity relationship techniques, based on statistical and machine learning methods such as multiple linear regression and partial least squares, were used with a novel pruning method for the selection of descriptors to develop robust models for both strains. Inspection of the dominant descriptors supports the hypothesis that chemical features that enable accumulation in the food vacuole of the parasite are key determinants of activity against both strains. The hydrophilic properties of the compounds were found to be crucial in predicting activity against the chloroquine-sensitive NF54 parasite strain, but not in the case of the chloroquine-resistant K1 strain, in line with previous studies. Additionally, the models suggest that ‘softer’ compounds tend to have improved activity for both strains than do ‘harder’ ones. The internally and externally validated models reported here should also prove useful in the future screening of potential antimalarial compounds for targeting chloroquine-resistant strains. Predictive models reveal linear relationships for activity of 4-aminoquinoline analogues active against chloroquine-sensitive strains of Plasmodium falciparum ![]()
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Affiliation(s)
| | - David L Cooper
- Department of Chemistry, University of Liverpool, Liverpool, L69 7ZD, UK
| | - Paul M O'Neill
- Department of Chemistry, University of Liverpool, Liverpool, L69 7ZD, UK
| | - Neil G Berry
- Department of Chemistry, University of Liverpool, Liverpool, L69 7ZD, UK.
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15
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Oliveira AA, Lipinski CF, Pereira EB, Honorio KM, Oliveira PR, Weber KC, Romero RAF, de Sousa AG, da Silva ABF. New consensus multivariate models based on PLS and ANN studies of sigma-1 receptor antagonists. J Mol Model 2017; 23:302. [PMID: 28971260 DOI: 10.1007/s00894-017-3444-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 08/18/2017] [Indexed: 10/18/2022]
Abstract
The treatment of neuropathic pain is very complex and there are few drugs approved for this purpose. Among the studied compounds in the literature, sigma-1 receptor antagonists have shown to be promising. In order to develop QSAR studies applied to the compounds of 1-arylpyrazole derivatives, multivariate analyses have been performed in this work using partial least square (PLS) and artificial neural network (ANN) methods. A PLS model has been obtained and validated with 45 compounds in the training set and 13 compounds in the test set (r2training = 0.761, q2 = 0.656, r2test = 0.746, MSEtest = 0.132 and MAEtest = 0.258). Additionally, multi-layer perceptron ANNs (MLP-ANNs) were employed in order to propose non-linear models trained by gradient descent with momentum backpropagation function. Based on MSEtest values, the best MLP-ANN models were combined in a MLP-ANN consensus model (MLP-ANN-CM; r2test = 0.824, MSEtest = 0.088 and MAEtest = 0.197). In the end, a general consensus model (GCM) has been obtained using PLS and MLP-ANN-CM models (r2test = 0.811, MSEtest = 0.100 and MAEtest = 0.218). Besides, the selected descriptors (GGI6, Mor23m, SRW06, H7m, MLOGP, and μ) revealed important features that should be considered when one is planning new compounds of the 1-arylpyrazole class. The multivariate models proposed in this work are definitely a powerful tool for the rational drug design of new compounds for neuropathic pain treatment. Graphical abstract Main scaffold of the 1-arylpyrazole derivatives and the selected descriptors.
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Affiliation(s)
- Aline A Oliveira
- Instituto de Química de São Carlos, Universidade de São Paulo, Av. Trabalhador São-Carlense 400, São Carlos, SP, 13560-970, Brazil
- Escola de Artes, Ciências e Humanidades, Universidade de São Paulo, Av. Arlindo Bettio, 1000, São Paulo, SP, 03828-000, Brazil
| | - Célio F Lipinski
- Instituto de Química de São Carlos, Universidade de São Paulo, Av. Trabalhador São-Carlense 400, São Carlos, SP, 13560-970, Brazil
| | - Estevão B Pereira
- Instituto de Química de São Carlos, Universidade de São Paulo, Av. Trabalhador São-Carlense 400, São Carlos, SP, 13560-970, Brazil
| | - Kathia M Honorio
- Escola de Artes, Ciências e Humanidades, Universidade de São Paulo, Av. Arlindo Bettio, 1000, São Paulo, SP, 03828-000, Brazil
| | - Patrícia R Oliveira
- Escola de Artes, Ciências e Humanidades, Universidade de São Paulo, Av. Arlindo Bettio, 1000, São Paulo, SP, 03828-000, Brazil
| | - Karen C Weber
- Centro de Ciências Exatas e da Natureza, Universidade Federal da Paraíba, Cidade Universitária, João Pessoa, PB, 58051-970, Brazil
| | - Roseli A F Romero
- Instituto de Ciências Matemáticas e de Computação, Universidade de São Paulo, Av. Trabalhador São-Carlense 400, São Carlos, SP, 13560-970, Brazil
| | - Alexsandro G de Sousa
- Universidade Estadual do Sudoeste da Bahia, Rodovia BR 415, Km 03, S/N, Itapetinga, BA, 45700-000, Brazil
| | - Albérico B F da Silva
- Instituto de Química de São Carlos, Universidade de São Paulo, Av. Trabalhador São-Carlense 400, São Carlos, SP, 13560-970, Brazil.
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16
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Isayev O, Oses C, Toher C, Gossett E, Curtarolo S, Tropsha A. Universal fragment descriptors for predicting properties of inorganic crystals. Nat Commun 2017; 8:15679. [PMID: 28580961 PMCID: PMC5465371 DOI: 10.1038/ncomms15679] [Citation(s) in RCA: 171] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 04/11/2017] [Indexed: 12/23/2022] Open
Abstract
Although historically materials discovery has been driven by a laborious trial-and-error process, knowledge-driven materials design can now be enabled by the rational combination of Machine Learning methods and materials databases. Here, data from the AFLOW repository for ab initio calculations is combined with Quantitative Materials Structure-Property Relationship models to predict important properties: metal/insulator classification, band gap energy, bulk/shear moduli, Debye temperature and heat capacities. The prediction's accuracy compares well with the quality of the training data for virtually any stoichiometric inorganic crystalline material, reciprocating the available thermomechanical experimental data. The universality of the approach is attributed to the construction of the descriptors: Property-Labelled Materials Fragments. The representations require only minimal structural input allowing straightforward implementations of simple heuristic design rules.
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Affiliation(s)
- Olexandr Isayev
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Corey Oses
- Center for Materials Genomics, Duke University, Durham, North Carolina 27708, USA
| | - Cormac Toher
- Center for Materials Genomics, Duke University, Durham, North Carolina 27708, USA
| | - Eric Gossett
- Center for Materials Genomics, Duke University, Durham, North Carolina 27708, USA
| | - Stefano Curtarolo
- Center for Materials Genomics, Duke University, Durham, North Carolina 27708, USA
- Materials Science, Electrical Engineering, Physics and Chemistry, Duke University, Durham, North Carolina 27708, USA
| | - Alexander Tropsha
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, USA
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García-García A, Gálvez J, de Julián-Ortiz JV, García-Domenech R, Muñoz C, Guna R, Borrás R. Search of Chemical Scaffolds for Novel Antituberculosis Agents. ACTA ACUST UNITED AC 2016; 10:206-14. [PMID: 15809316 DOI: 10.1177/1087057104273486] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
A method to identify chemical scaffolds potentially active against Mycobacterium tuberculosis is presented. The molecular features of a set of structurally heterogeneous antituberculosis drugs were coded by means of structural invariants. Three techniques were used to obtain equations able to model the antituberculosis activity: linear discriminant analysis, multilinear regression, and shrinkage estimation–ridge regression. The model obtained was statistically validated through leave- n-out test, and an external set and was applied to a database for the search of new active agents. The selected compounds were assayed in vitro, and among those identified as active stand reserpine, N,N,N′,N′-tetrakis-(2-pyridylmethyl)-ethylenediamine (TPEN), trifluoperazine, pentamidine, and 2-methyl-4,6-dinitro-phenol (DNOC). They show activity comparable to or superior to ethambutol, used in combination with other drugs for the prevention and treatment of Mycobacterium avium complex and drug-resistant tuberculosis.
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Affiliation(s)
- Angeles García-García
- Unidad de Investigación de Diseño de Fármacos y Conectividad Molecular, Departamento de Química Física, Facultad de Farmacia, Universitat de València, Av. Vicent Andrés Estellés s/n, 46100 Burjassot, Spain
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18
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Patel RV, Mistry B, Syed R, Rathi AK, Lee YJ, Sung JS, Shinf HS, Keum YS. Chrysin-piperazine conjugates as antioxidant and anticancer agents. Eur J Pharm Sci 2016; 88:166-77. [PMID: 26924226 DOI: 10.1016/j.ejps.2016.02.011] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 01/30/2016] [Accepted: 02/20/2016] [Indexed: 11/17/2022]
Abstract
Synthesis of 7-(4-bromobutoxy)-5-hydroxy-2-phenyl-4H-chromen-4-one intermediate treating chrysin with 1,4-dibromobutane facilitated combination of chrysin with a wide range of piperazine moieties which were equipped via reacting the corresponding amines with bis(2-chloroethyl)amine hydrochloride in diethylene glycol monomethyl ether solvent. Free radical scavenging potential of prepared products was analyzed in vitro adopting DPPH and ABTS bioassay in addition to the evaluation of in vitro anticancer efficacies against cervical cancer cell lines (HeLa and CaSki) and an ovarian cancer cell line SK-OV-3 using SRB assay. Bearable toxicity of 7a-w was examined employing Madin-Darby canine kidney (MDCK) cell line. In addition, cytotoxic nature of the presented compounds was inspected utilizing Human bone marrow derived mesenchymal stem cells (hBM-MSCs). Overall, 7a-w indicated remarkable antioxidant power in scavenging DPPH(·) and ABTS(·+), particularly analogs 7f, 7j, 7k, 7l, 7n, 7q, 7v, 7w have shown promising free radical scavenging activity. Analogs 7j and 7o are identified to be highly active candidates against HeLa and CaSki cell lines, whereas 7h and 7l along with 7j proved to be very sensitive towards ovarian cancer cell line SKOV-3. None of the newly prepared scaffolds showed cytotoxic nature toward hBM-MSCs cells. From the structure-activity point of view, nature and position of the electron withdrawing and electron donating functional groups on the piperazine core may contribute to the anticipated antioxidant and anticancer action. Different spectroscopic techniques (FT-IR, (1)H NMR, (13)C NMR, Mass) and elemental analysis (CHN) were utilized to confirm the desired structure of final compounds.
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Affiliation(s)
- Rahul V Patel
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany ASCR & Palacky´ University, Šlechtitelu° 27, 783 71 Olomouc, Czech Republic; Department of Food Science and Biotechnology, Dongguk University, Biomedical Campus, 32 Dongguk-ro, Ilsandong-gu, Goyang-si, Gyenggi-do, Republic of Korea.
| | - Bhupendra Mistry
- Organic Research Laboratory, Department of Bioresources and Food Sciences, College of Life and Environmental Sciences, Konkuk University, Seoul, Republic of Korea
| | - Riyaz Syed
- Department of Chemistry, J.N.T. University, Kukatpally, Hyderabad 500 085, India
| | - Anuj K Rathi
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University, Šlechtitelů 11, Olomouc, Czech Republic
| | - Yoo-Jung Lee
- Department of Life Science, Dongguk University, Goyang, Gyeonggi-do 10326, Republic of Korea
| | - Jung-Suk Sung
- Department of Life Science, Dongguk University, Goyang, Gyeonggi-do 10326, Republic of Korea
| | - Han-Seung Shinf
- Department of Food Science and Biotechnology, Dongguk University, Biomedical Campus, 32 Dongguk-ro, Ilsandong-gu, Goyang-si, Gyenggi-do, Republic of Korea
| | - Young-Soo Keum
- Organic Research Laboratory, Department of Bioresources and Food Sciences, College of Life and Environmental Sciences, Konkuk University, Seoul, Republic of Korea.
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Zanni R, Galvez-Llompart M, García-Domenech R, Galvez J. Latest advances in molecular topology applications for drug discovery. Expert Opin Drug Discov 2015; 10:945-57. [DOI: 10.1517/17460441.2015.1062751] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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20
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Predicting antiprotozoal activity of benzyl phenyl ether diamine derivatives through QSAR multi-target and molecular topology. Mol Divers 2015; 19:357-66. [DOI: 10.1007/s11030-015-9575-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 02/22/2015] [Indexed: 01/12/2023]
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21
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Halder AK, Saha A, Saha KD, Jha T. Stepwise development of structure–activity relationship of diverse PARP-1 inhibitors through comparative and validatedin silico modeling techniques and molecular dynamics simulation. J Biomol Struct Dyn 2014; 33:1756-79. [DOI: 10.1080/07391102.2014.969772] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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22
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Caboni L, Gálvez-Llompart M, Gálvez J, Blanco F, Rubio-Martinez J, Fayne D, Lloyd DG. Molecular topology applied to the discovery of 1-benzyl-2-(3-fluorophenyl)-4-hydroxy-3-(3-phenylpropanoyl)-2H-pyrrole-5-one as a non-ligand-binding-pocket antiandrogen. J Chem Inf Model 2014; 54:2953-66. [PMID: 25233256 DOI: 10.1021/ci500324f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report the discovery of 1-benzyl-2-(3-fluorophenyl)-4-hydroxy-3-(3-phenylpropanoyl)-2H-pyrrole-5-one as a novel non-ligand binding pocket (non-LBP) antagonist of the androgen receptor (AR) through the application of molecular topology techniques. This compound, validated through time-resolved fluorescence resonance energy transfer and fluorescence polarization biological assays, provides the basis for lead optimization and structure-activity relationship analysis of a new series of non-LBP AR antagonists. Induced-fit docking and molecular dynamics studies have been performed to establish a consistent hypothesis for the interaction of the new active molecule on the AR surface.
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Affiliation(s)
- Laura Caboni
- Molecular Design Group, School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin , Dublin 2, Ireland
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23
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Xi L, Li S, Yao X, Wei Y, Li J, Liu H, Wu X. In SilicoStudy Combining Docking and QSAR Methods on a Series of Matrix Metalloproteinase 13 Inhibitors. Arch Pharm (Weinheim) 2014; 347:825-33. [PMID: 25363411 DOI: 10.1002/ardp.201400200] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2014] [Revised: 07/01/2014] [Accepted: 07/03/2014] [Indexed: 11/09/2022]
Affiliation(s)
- Lili Xi
- Department of Pharmacy; First Hospital of Lanzhou University; Lanzhou China
| | - Shuyan Li
- Department of Chemistry; Lanzhou University; Lanzhou China
| | - Xiaojun Yao
- Department of Chemistry; Lanzhou University; Lanzhou China
| | - Yuhui Wei
- Department of Pharmacy; First Hospital of Lanzhou University; Lanzhou China
| | - Jiazhong Li
- School of Pharmacy; Lanzhou University; Lanzhou China
| | - Huanxiang Liu
- School of Pharmacy; Lanzhou University; Lanzhou China
| | - Xin'an Wu
- Department of Pharmacy; First Hospital of Lanzhou University; Lanzhou China
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Wang J, Land D, Ono K, Galvez J, Zhao W, Vempati P, Steele JW, Cheng A, Yamada M, Levine S, Mazzola P, Pasinetti GM. Molecular topology as novel strategy for discovery of drugs with aβ lowering and anti-aggregation dual activities for Alzheimer's disease. PLoS One 2014; 9:e92750. [PMID: 24671215 PMCID: PMC3966818 DOI: 10.1371/journal.pone.0092750] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Accepted: 02/19/2014] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND AND PURPOSE In this study, we demonstrate the use of Molecular topology (MT) in an Alzheimer's disease (AD) drug discovery program. MT uses and expands upon the principles governing the molecular connectivity theory of numerically characterizing molecular structures, in the present case, active anti-AD drugs/agents, using topological descriptors to build models. Topological characterization has been shown to embody sufficient molecular information to provide strong correlation to therapeutic efficacy. EXPERIMENTAL APPROACH We used MT to include multiple bioactive properties that allows for the identification of multi-functional single agent compounds, in this case, the dual functions of β-amyloid (Aβ) -lowering and anti-oligomerization. Using this technology, we identified and designed novel compounds in chemical classes unrelated to current anti-AD agents that exert dual Aβ lowering and anti-Aβ oligomerization activities in animal models of AD. AD is a multifaceted disease with different pathological features. CONCLUSION AND IMPLICATIONS Our study, for the first time, demonstrated that MT can provide novel strategy for discovering drugs with Aβ lowering and anti-aggregation dual activities for AD.
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Affiliation(s)
- Jun Wang
- Department of Neurology, Mount Sinai School of Medicine, New York, New York, United States of America
- Geriatric Research, Education and Clinical Center, James J. Peters Veterans Affairs Medical Center, Bronx, New York New York, United States of America
| | - David Land
- Medisyn Technologies, Inc. Minnetonka, Minnesota, United States of America
| | - Kenjiro Ono
- Department of Neurology and Neurobiology of Aging, Kanazawa University, Kanazawa, Japan
| | - Jorge Galvez
- Molecular Topology & Drug Design Unit, University of Valencia, Valencia, Spain
| | - Wei Zhao
- Department of Neurology, Mount Sinai School of Medicine, New York, New York, United States of America
| | - Prashant Vempati
- Department of Neurology, Mount Sinai School of Medicine, New York, New York, United States of America
| | - John W. Steele
- Department of Neurology, Mount Sinai School of Medicine, New York, New York, United States of America
| | - Alice Cheng
- Department of Neurology, Mount Sinai School of Medicine, New York, New York, United States of America
| | - Masahito Yamada
- Department of Neurology and Neurobiology of Aging, Kanazawa University, Kanazawa, Japan
| | - Samara Levine
- Department of Neurology, Mount Sinai School of Medicine, New York, New York, United States of America
| | - Paolo Mazzola
- Department of Neurology, Mount Sinai School of Medicine, New York, New York, United States of America
| | - Giulio M. Pasinetti
- Department of Neurology, Mount Sinai School of Medicine, New York, New York, United States of America
- Geriatric Research, Education and Clinical Center, James J. Peters Veterans Affairs Medical Center, Bronx, New York New York, United States of America
- * E-mail:
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Abstract
Computer-aided drug discovery/design methods have played a major role in the development of therapeutically important small molecules for over three decades. These methods are broadly classified as either structure-based or ligand-based methods. Structure-based methods are in principle analogous to high-throughput screening in that both target and ligand structure information is imperative. Structure-based approaches include ligand docking, pharmacophore, and ligand design methods. The article discusses theory behind the most important methods and recent successful applications. Ligand-based methods use only ligand information for predicting activity depending on its similarity/dissimilarity to previously known active ligands. We review widely used ligand-based methods such as ligand-based pharmacophores, molecular descriptors, and quantitative structure-activity relationships. In addition, important tools such as target/ligand data bases, homology modeling, ligand fingerprint methods, etc., necessary for successful implementation of various computer-aided drug discovery/design methods in a drug discovery campaign are discussed. Finally, computational methods for toxicity prediction and optimization for favorable physiologic properties are discussed with successful examples from literature.
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Affiliation(s)
- Gregory Sliwoski
- Jr., Center for Structural Biology, 465 21st Ave South, BIOSCI/MRBIII, Room 5144A, Nashville, TN 37232-8725.
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The derivation of a chiral substituent code for secondary alcohols and its application to the prediction of enantioselectivity. J Mol Graph Model 2013; 43:11-20. [DOI: 10.1016/j.jmgm.2013.03.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Revised: 03/21/2013] [Accepted: 03/23/2013] [Indexed: 11/23/2022]
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27
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Galvez J, Galvez-Llompart M, Zanni R, Garcia-Domenech R. Advances in the molecular modeling and quantitative structure–activity relationship-based design for antihistamines. Expert Opin Drug Discov 2013; 8:305-17. [DOI: 10.1517/17460441.2013.748745] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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28
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Gálvez J, Gálvez-Llompart M, García-Domenech R. Molecular topology as a novel approach for drug discovery. Expert Opin Drug Discov 2012; 7:133-53. [PMID: 22468915 DOI: 10.1517/17460441.2012.652083] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
INTRODUCTION Molecular topology (MT) has emerged in recent years as a powerful approach for the in silico generation of new drugs. One key part of MT is that, in the process of drug design/discovery, there is no need for an explicit knowledge of a drug's mechanism of action unlike other drug discovery methods. AREAS COVERED In this review, the authors introduce the topic by explaining briefly the most common methodology used today in drug design/discovery and address the most important concepts of MT and the methodology followed (QSAR equations, LDA, etc.). Furthermore, the significant results achieved, from this approach, are outlined and discussed. EXPERT OPINION The results outlined herein can be explained by considering that MT represents a new paradigm in the field of drug design. This means that it is not only an alternative method to the conventional methods, but it is also independent, that is, it represents a pathway to connect directly molecular structure with the experimental properties of the compounds (particularly drugs). Moreover, the process can be realized also in the reverse pathway, that is, designing new molecules from their topological pattern, what opens almost limitless expectations in new drugs development, given that the virtual universe of molecules is much greater than that of the existing ones.
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Affiliation(s)
- Jorge Gálvez
- University of Valencia Avd, Department of Physical Chemistry, Molecular Connectivity and Drug Design Research Unit, Valencia, Spain.
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29
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Rastija V, Bešlo D, Nikolić S. Two-dimensional quantitative structure–activity relationship study on polyphenols as inhibitors of α-glucosidase. Med Chem Res 2011. [DOI: 10.1007/s00044-011-9938-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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30
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Lather V, Madan AK. Predicting Acyl-Coenzyme A: Cholesterol O-Acyltransferase Inhibitory Activity: Computational Approach Using Topological Descriptors. ACTA ACUST UNITED AC 2011. [DOI: 10.3109/10559610390464124] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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31
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Discovery of novel anti-inflammatory drug-like compounds by aligning in silico and in vivo screening: The nitroindazolinone chemotype. Eur J Med Chem 2011; 46:5736-53. [DOI: 10.1016/j.ejmech.2011.07.053] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Revised: 07/28/2011] [Accepted: 07/29/2011] [Indexed: 11/15/2022]
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32
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Gupta M, Gupta S, Dureja H, Madan AK. Superaugmented Eccentric Distance Sum Connectivity Indices: Novel Highly Discriminating Topological Descriptors for QSAR/QSPR. Chem Biol Drug Des 2011; 79:38-52. [DOI: 10.1111/j.1747-0285.2011.01264.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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33
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Nekoei M, Salimi M, Dolatabadi M, Mohammadhosseini M. Prediction of antileukemia activity of berbamine derivatives by genetic algorithm–multiple linear regression. MONATSHEFTE FUR CHEMIE 2011. [DOI: 10.1007/s00706-011-0510-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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34
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Moorthy NSHN, Ramos MJ, Fernandes PA. Topological, hydrophobicity, and other descriptors on α-glucosidase inhibition: a QSAR study on xanthone derivatives. J Enzyme Inhib Med Chem 2011; 26:755-66. [PMID: 21284409 DOI: 10.3109/14756366.2010.549089] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Quantitative structure activity relationship analysis was performed on a series of xanthone derivatives to establish the structural features required for α-glucosidase inhibitory activity. The computational and statistical analysis was performed with V life MDS (Molecular Design Suite) and Statistica software. The selected models show significant predictive power, stability, and reliability in terms of cross-validated correlation coefficient (Q(2)(cv) > 0.74 and Q(2)(test) > 0.5) and other validation parameters. The results show that the SaaaC count, MMFF_6 and dipole moment are mainly contributed for the activity along with the hydrophobicity descriptors. It describes that heteroatoms (oxygen atom connected with carbon atom) in the molecules are favourable for α-glucosidase inhibitory activity. The E-state count descriptor suggests that when carbon atoms connected with three aromatic bonds and hydrogen or other atoms are favourable for the activity. The SAHA and SAMH descriptors show that the hydrophilic area in the molecule is important for the activity while high hydrophilicity is unfavourable for the activity. This study concluded that hydrophilic, polar and/or electron negative groups, which are responsible for hydrogen bonding and interaction with the enzyme for favourable activity.
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Affiliation(s)
- N S Hari Narayana Moorthy
- REQUIMTE, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, Porto, Portugal.
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35
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QSAR studies on a number of pyrrolidin-2-one antiarrhythmic arylpiperazinyls. Med Chem Res 2011; 21:373-381. [PMID: 22308062 PMCID: PMC3265727 DOI: 10.1007/s00044-010-9540-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2010] [Accepted: 12/10/2010] [Indexed: 12/18/2022]
Abstract
The activity of a number of 1-[3-(4-arylpiperazin-1-yl)propyl]pyrrolidin-2-one antiarrhythmic (AA) agents was described using the quantitative structure–activity relationship model by applying it to 33 compounds. The molecular descriptors of the AA activity were obtained by quantum chemical calculations combined with molecular modeling calculations. The resulting model explains up to 91% of the variance and it was successfully validated by four tests (LOO, LMO, external test, and Y-scrambling test). Statistical analysis shows that the AA activity of the studied compounds depends mainly on the PCR and JGI4 descriptors.
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36
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Mallakpour S, Hatami M, Golmohammadi H. Theoretical study on modeling and prediction of optical rotation for biodegradable polymers containing α-amino acids using QSAR approaches. J Mol Model 2010; 17:1743-53. [DOI: 10.1007/s00894-010-0885-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2010] [Accepted: 10/20/2010] [Indexed: 11/29/2022]
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37
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MT103 inhibits tumor growth with minimal toxicity in murine model of lung carcinoma via induction of apoptosis. Invest New Drugs 2010; 29:846-52. [DOI: 10.1007/s10637-010-9432-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2010] [Accepted: 04/06/2010] [Indexed: 11/26/2022]
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38
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Sharma BK, Singh P, Sarbhai K, Prabhakar YS. A quantitative structure-activity relationship study on serotonin 5-HT6) receptor ligands: indolyl and piperidinyl sulphonamides. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2010; 21:369-388. [PMID: 20544556 DOI: 10.1080/10629361003773997] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The serotonin 5-HT(6) binding affinity of indolyl- and piperidinyl-sulphonamide derivatives has been analysed with topological and molecular features with DRAGON software. Analysis of the structural features in conjunction with the biological endpoints in combinatorial protocol in multiple linear regression (CP-MLR) led to the identification of 25 descriptors for modelling the activity. The study clearly suggested the role of an average Randic-type eigenvector-based index from adjacency matrix, VRA2, number of secondary aliphatic amines, nNHR, the sum of the topological distance between N and O, T(N...O), ring tertiary carbon atoms, nCrHR, and CH2RX type fragment, C-006, in a molecular structure to optimize the 5-HT(6) binding affinities of titled compounds. The PLS analysis confirmed the dominance of information content of CP-MLR identified descriptors for modelling the activity when compared with those of leftover ones.
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Affiliation(s)
- B K Sharma
- Department of Chemistry, S.K. Government College, Sikar-332 001, India.
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39
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Mercader AG, Pomilio AB. QSAR study of flavonoids and biflavonoids as influenza H1N1 virus neuraminidase inhibitors. Eur J Med Chem 2010; 45:1724-30. [PMID: 20116898 DOI: 10.1016/j.ejmech.2010.01.005] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2009] [Revised: 12/30/2009] [Accepted: 01/05/2010] [Indexed: 11/25/2022]
Abstract
We performed a predictive analysis based on Quantitative Structure-Activity Relationships (QSAR) of a very important property of flavonoids which is the inhibition (IC50) of influenza H1N1 virus neuraminidase. The best linear model constructed from 20 molecular structures incorporated four molecular descriptors, selected from more than a thousand geometrical, topological, quantum-mechanical and electronic types of descriptors. The obtained model suggests that the activity depends on the electric charges, masses and polarizabilities of the atoms present in the molecule as well as its conformation. The model showed good predictive ability established by the theoretical and external test set validations.
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Affiliation(s)
- Andrew G Mercader
- PRALIB (UBA-CONICET), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, C1113AAD Buenos Aires, Argentina.
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40
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Asadabadi EB, Abdolmaleki P, Barkooie SMH, Jahandideh S, Rezaei MA. A combinatorial feature selection approach to describe the QSAR of dual site inhibitors of acetylcholinesterase. Comput Biol Med 2009; 39:1089-95. [DOI: 10.1016/j.compbiomed.2009.09.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2009] [Accepted: 09/12/2009] [Indexed: 10/20/2022]
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41
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Nikolic K, Agababa D. Prediction of hepatic microsomal intrinsic clearance and human clearance values for drugs. J Mol Graph Model 2009; 28:245-52. [DOI: 10.1016/j.jmgm.2009.08.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2009] [Revised: 07/20/2009] [Accepted: 08/03/2009] [Indexed: 11/16/2022]
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42
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Jasinski P, Zwolak P, Terai K, Borja-Cacho D, Dudek AZ. PKC-alpha inhibitor MT477 slows tumor growth with minimal toxicity in in vivo model of non-Ras-mutated cancer via induction of apoptosis. Invest New Drugs 2009; 29:33-40. [DOI: 10.1007/s10637-009-9330-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2009] [Accepted: 09/16/2009] [Indexed: 11/29/2022]
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43
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Chen X, Liang YZ, Yuan DL, Xu QS. A modified uncorrelated linear discriminant analysis model coupled with recursive feature elimination for the prediction of bioactivity. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2009; 20:1-26. [PMID: 19343582 DOI: 10.1080/10629360902724127] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
To meet the requirements of providing accurate, robust, and interpretable prediction of bioactivity, a modified uncorrelated linear discriminant analysis (M-ULDA) model was developed. In addition, a feature selection method called recursive feature elimination (RFE), originally used for support vector machine (SVM), was introduced and modified to fit the scheme of ULDA. From the evaluation of six pharmaceutical datasets, the M-UDLA coupled with RFE showed better or comparable classification accuracy with respect to other well-studied methods such as SVM and decision trees. The RFE used for ULDA has the advantage of increasing the computational speed and provides useful insights into biochemical mechanisms related to pharmaceutical activity by significantly reducing the number of variables used for the final model.
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Affiliation(s)
- X Chen
- College of Chemistry and Chemical Engineering, Central South University, Changsha, People's Republic of China
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44
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Smith J, Stein V. SPORCalc: A development of a database analysis that provides putative metabolic enzyme reactions for ligand-based drug design. Comput Biol Chem 2008; 33:149-59. [PMID: 19157988 DOI: 10.1016/j.compbiolchem.2008.11.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2008] [Accepted: 11/12/2008] [Indexed: 10/21/2022]
Abstract
Understanding both the enzyme reactions that contribute to intermediate metabolism and the biochemical fate of candidate therapeutic and toxic agents are essential for drug design. Traditional metabolic databases indicate whether reactions have been observed but do not provide the likelihoods of reactions occurring, for example those of mixed function oxygenases and oxidases, during phase I metabolism. The desire for more quantitative predictions motivated the development of the recently introduced Substrate Product Occurrence Ratio Calculator (SPORCalc) that identifies metabolically labile atom positions in candidate compounds. This paper describes a further development and provides a clearer explanation of SPORCalc for the computational pharmacology, medicinal chemistry and drug design communities interested in metabolic prediction of xenobiotics using chemical databases of biotransformations. Examples of reaction centre detection in Metabolite are described followed by a demonstration of almokalant, an anti-arrhythmic agent, undergoing phase I metabolism. In general, occurrence ratio (OR) values are calculated throughout a compound and its transformed metabolites to give propensity (p) values at each atom position. The OR values from substrates and products in the database are essential for addition and elimination reactions. For almokalant, the resulting p values ranged from 10(-1) to 10(-5) and their order of magnitude reflected the known and experimentally observed metabolites. SPORCalc depends entirely on the level of detail from isoform- or species-specific reaction classes in Metabolite. Labile atom positions (sites of metabolism) are identified in both the candidate compound and its metabolites. In general, the likelihood of one enzyme isoform-dependent reaction occurring relative to another and the putative metabolic routes from different isoforms can be investigated. SPORCalc can be developed further to include suitable three-dimensional, structure-activity and physiochemical information.
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Affiliation(s)
- James Smith
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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45
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Rivera-Borroto O, Marrero-Ponce Y, Meneses-Marcel A, Escario J, Gómez Barrio A, Arán V, Martins Alho M, Montero Pereira D, Nogal J, Torrens F, Ibarra-Velarde F, Montenegro Y, Huesca-Guillén A, Rivera N, Vogel C. Discovery of Novel Trichomonacidals Using LDA-Driven QSAR Models and Bond-Based Bilinear Indices as Molecular Descriptors. ACTA ACUST UNITED AC 2008. [DOI: 10.1002/qsar.200610165] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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46
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Jasinski P, Zwolak P, Terai K, Dudek AZ. Novel Ras pathway inhibitor induces apoptosis and growth inhibition of K-ras-mutated cancer cells in vitro and in vivo. Transl Res 2008; 152:203-12. [PMID: 19010291 DOI: 10.1016/j.trsl.2008.09.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2008] [Revised: 08/23/2008] [Accepted: 09/04/2008] [Indexed: 10/21/2022]
Abstract
MT477 is a novel quinoline with potential activity in Ras-mutated cancers. In this study, MT477 preferentially inhibited the proliferation of K-ras-mutated human pulmonary (A549) and pancreatic (MiaPaCa-2) adenocarcinoma cell lines, compared with a non-Ras-mutated human lung squamous carcinoma cell line (H226) and normal human lung fibroblasts. MT477 treatment induced apoptosis in A549 cells and was associated with caspase-3 activation. MT477 also induced sub-G1 cell-cycle arrest in A549 cells. Although we found that MT477 partially inhibited protein kinase C (PKC), it inhibited Ras directly followed in time by inhibition of 2 Ras downstream molecules, Erk1/2 and Ral. MT477 also caused a reorganization of the actin cytoskeleton and formation of filopodias in A549 cells; this event may lead to decreased migration and invasion of tumor cells. In a xenograft mouse model, A549 tumor growth was inhibited significantly by MT477 at a dose of 1 mg/kg (P < 0.05 vs vehicle control). Taken together, these results support the conclusion that MT477 acts as a direct Ras inhibitor. This quinoline, therefore, could potentially be active in Ras-mutated cancers and could be developed extensively as an anticancer molecule with this in mind.
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Affiliation(s)
- Piotr Jasinski
- Division of Hematology, Oncology and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, Minn. 55455, USA
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47
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Meneses-Marcel A, Rivera-Borroto OM, Marrero-Ponce Y, Montero A, Machado Tugores Y, Escario JA, Gómez Barrio A, Montero Pereira D, Nogal JJ, Kouznetsov VV, Ochoa Puentes C, Bohórquez AR, Grau R, Torrens F, Ibarra-Velarde F, Arán VJ. New antitrichomonal drug-like chemicals selected by bond (edge)-based TOMOCOMD-CARDD descriptors. ACTA ACUST UNITED AC 2008; 13:785-94. [PMID: 18753687 DOI: 10.1177/1087057108323122] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Bond-based quadratic indices, new TOMOCOMD-CARDD molecular descriptors, and linear discriminant analysis (LDA) were used to discover novel lead trichomonacidals. The obtained LDA-based quantitative structure-activity relationships (QSAR) models, using nonstochastic and stochastic indices, were able to classify correctly 87.91% (87.50%) and 89.01% (84.38%) of the chemicals in training (test) sets, respectively. They showed large Matthews correlation coefficients of 0.75 (0.71) and 0.78 (0.65) for the training (test) sets, correspondingly. Later, both models were applied to the virtual screening of 21 chemicals to find new lead antitrichomonal agents. Predictions agreed with experimental results to a great extent because a correct classification for both models of 95.24% (20 of 21) of the chemicals was obtained. Of the 21 compounds that were screened and synthesized, 2 molecules (chemicals G-1, UC-245) showed high to moderate cytocidal activity at the concentration of 10 microg/ml, another 2 compounds (G-0 and CRIS-148) showed high cytocidal activity only at the concentration of 100 microg/ml, and the remaining chemicals (from CRIS-105 to CRIS-153, except CRIS-148) were inactive at these assayed concentrations. Finally, the best candidate, G-1 (cytocidal activity of 100% at 10 microg/ml) was in vivo assayed in ovariectomized Wistar rats achieving promising results as a trichomonacidal drug-like compound.
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Affiliation(s)
- Alfredo Meneses-Marcel
- Unit of Computer-Aided Molecular Biosilico Discovery and Bioinformatic Research (CAMD-BIR Unit), Faculty of Chemistry-Pharmacy, Central University of Las Villas, Villa Clara, Cuba
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48
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Marrero-Ponce Y, Meneses-Marcel A, Rivera-Borroto OM, García-Domenech R, De Julián-Ortiz JV, Montero A, Escario JA, Barrio AG, Pereira DM, Nogal JJ, Grau R, Torrens F, Vogel C, Arán VJ. Bond-based linear indices in QSAR: computational discovery of novel anti-trichomonal compounds. J Comput Aided Mol Des 2008; 22:523-40. [DOI: 10.1007/s10822-008-9171-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2006] [Accepted: 01/05/2008] [Indexed: 10/22/2022]
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49
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Castillo-Garit JA, Marrero-Ponce Y, Torrens F, García-Domenech R. Estimation of ADME Properties in Drug Discovery: Predicting Caco-2 Cell Permeability Using Atom-Based Stochastic and Non-stochastic Linear Indices. J Pharm Sci 2008; 97:1946-76. [PMID: 17724669 DOI: 10.1002/jps.21122] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The in vitro determination of the permeability through cultured Caco-2 cells is the most often-used in vitro model for drug absorption. In this report, we use the largest data set of measured P(Caco-2), consisting of 157 structurally diverse compounds. Linear discriminant analysis (LDA) was used to obtain quantitative models that discriminate higher absorption compounds from those with moderate-poorer absorption. The best LDA model has an accuracy of 90.58% and 84.21% for training and test set. The percentage of good correlation, in the virtual screening of 241 drugs with the reported values of the percentage of human intestinal absorption (HIA), was greater than 81%. In addition, multiple linear regression models were developed to predict Caco-2 permeability with determination coefficients of 0.71 and 0.72. Our method compares favorably with other approaches implemented in the Dragon software, as well as other methods from the international literature. These results suggest that the proposed method is a good tool for studying the oral absorption of drug candidates.
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Affiliation(s)
- Juan A Castillo-Garit
- Applied Chemistry Research Center, Central University of Las Villas, Santa Clara, 54830 Villa Clara, Cuba.
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50
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Mahmoudi N, Garcia-Domenech R, Galvez J, Farhati K, Franetich JF, Sauerwein R, Hannoun L, Derouin F, Danis M, Mazier D. New active drugs against liver stages of Plasmodium predicted by molecular topology. Antimicrob Agents Chemother 2008; 52:1215-20. [PMID: 18212104 PMCID: PMC2292524 DOI: 10.1128/aac.01043-07] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2007] [Revised: 10/31/2007] [Accepted: 01/13/2008] [Indexed: 11/20/2022] Open
Abstract
We conducted a quantitative structure-activity relationship (QSAR) study based on a database of 127 compounds previously tested against the liver stage of Plasmodium yoelii in order to develop a model capable of predicting the in vitro antimalarial activities of new compounds. Topological indices were used as structural descriptors, and their relation to antimalarial activity was determined by using linear discriminant analysis. A topological model consisting of two discriminant functions was created. The first function discriminated between active and inactive compounds, and the second identified the most active among the active compounds. The model was then applied sequentially to a large database of compounds with unknown activity against liver stages of Plasmodium. Seventeen drugs that were predicted to be active or inactive were selected for testing against the hepatic stage of P. yoelii in vitro. Antiretroviral, antifungal, and cardiotonic drugs were found to be highly active (nanomolar 50% inhibitory concentration values), and two ionophores completely inhibited parasite development. The 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay was performed on hepatocyte cultures for all compounds, and none of these compounds were toxic in vitro. For both ionophores, the same in vitro assay as those for P. yoelii has confirmed their in vitro activities on Plasmodium falciparum. A similar topological model was used to estimate the octanol/water partition of each compound. These results demonstrate the utility of the QSAR and molecular topology approaches for identifying new drugs that are active against the hepatic stage of malaria parasites. We also show the remarkable efficacy of some drugs that were not previously reported to have antiparasitic activity.
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Affiliation(s)
- Nassira Mahmoudi
- Université Pierre et Marie Curie-Paris 6, UMR S511, Paris F-75013, France.
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