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Le-Thi-Thu H, Marrero-Ponce Y, Casañola-Martin GM, Cardoso GC, Chávez M, Garcia MM, Morell C, Torrens F, Abad C. A Comparative Study of Nonlinear Machine Learning for the “In Silico” Depiction of Tyrosinase Inhibitory Activity from Molecular Structure. Mol Inform 2011; 30:527-37. [DOI: 10.1002/minf.201100021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2010] [Accepted: 03/25/2010] [Indexed: 11/05/2022]
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Casañola-Martin GM, Marrero-Ponce Y, Khan MTH, Khan SB, Torrens F, Pérez-Jiménez F, Rescigno A, Abad C. Bond-based 2D quadratic fingerprints in QSAR studies: virtual and in vitro tyrosinase inhibitory activity elucidation. Chem Biol Drug Des 2010; 76:538-45. [PMID: 20964806 DOI: 10.1111/j.1747-0285.2010.01032.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In this report, we show the results of quantitative structure-activity relationship (QSAR) studies of tyrosinase inhibitory activity, by using the bond-based quadratic indices as molecular descriptors (MDs) and linear discriminant analysis (LDA), to generate discriminant functions to predict the anti-tyrosinase activity. The best two models [Eqs (6) and (12)] out of the total 12 QSAR models developed here show accuracies of 93.51% and 91.21%, as well as high Matthews correlation coefficients (C) of 0.86 and 0.82, respectively, in the training set. The validation external series depicts values of 90.00% and 89.44% for these best two equations (6) and (12), respectively. Afterwards, a second external prediction data are used to perform a virtual screening of compounds reported in the literature as active (tyrosinase inhibitors). In a final step, a series of lignans is analysed using the in silico-developed models, and in vitro corroboration of the activity is carried out. An issue of great importance to remark here is that all compounds present greater inhibition values than Kojic acid (standard tyrosinase inhibitor: IC₅₀ = 16.67 μm). The current obtained results could be used as a framework to increase the speed, in the biosilico discovery of leads for the treatment of skin disorders.
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Le-Thi-Thu H, Casañola-Martín GM, Marrero-Ponce Y, Rescigno A, Saso L, Parmar VS, Torrens F, Abad C. Novel coumarin-based tyrosinase inhibitors discovered by OECD principles-validated QSAR approach from an enlarged, balanced database. Mol Divers 2010; 15:507-20. [PMID: 20814821 DOI: 10.1007/s11030-010-9274-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2010] [Accepted: 08/16/2010] [Indexed: 12/16/2022]
Abstract
The present work is devoted to the development and application of a multi-agent Quantitative Structure-Activity Relationship (QSAR) classification system for tyrosinase inhibitor identification, in which the individual QSAR outputs are the inputs of a fusion approach based on the voting mechanism. The individual models are based on TOMOCOMD-CARDD (TOpological Molecular COMputational Design-Computer Aided Rational Drug Design) atom-based bilinear descriptors and Linear Discriminant Analysis (LDA) on a novel enlarged, balanced database of 1,429 compounds within 701 greatly dissimilar molecules presenting anti-tyrosinase activity. A total of 21 adequate models are obtained taking into account the requirements of the Organization for Economic Cooperation and Development (OECD) principles for QSAR validation and present global accuracies (Q) above 84.50 and 79.27% in the training and test sets, respectively. The resulted fusion system is used for the in silico identification of synthesized coumarin derivatives as novel tyrosinase inhibitors. The 7-hydroxycoumarin (compound C07) shows potent activity for the inhibition of monophenolase activity of mushroom tyrosinase giving a value of inhibition percentage close to 100% in vitro assays, by means of spectrophotometric analysis. The current report could help to shed some clues in the identification of new chemicals that inhibit tyrosinase enzyme, for entering in the pipeline of drug discovery development.
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Marrero-Ponce Y, M. Casanola-Martin G, Tareq Hassan Khan M, Torrens F, Rescigno A, Abad C. Ligand-Based Computer-Aided Discovery of Tyrosinase Inhibitors. Applications of the TOMOCOMD-CARDD Method to the Elucidation of New Compounds. Curr Pharm Des 2010; 16:2601-24. [DOI: 10.2174/138161210792389216] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2010] [Accepted: 06/30/2010] [Indexed: 11/22/2022]
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Ortega-Broche SE, Marrero-Ponce Y, Díaz YE, Torrens F, Pérez-Giménez F. tomocomd-camps and protein bilinear indices - novel bio-macromolecular descriptors for protein research: I. Predicting protein stability effects of a complete set of alanine substitutions in the Arc repressor. FEBS J 2010; 277:3118-46. [DOI: 10.1111/j.1742-4658.2010.07711.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Torrens F, Castellano G. Protein negative/positively cooperative binding to zwitterionic/anionic vesicles. J Cheminform 2010. [PMCID: PMC2867144 DOI: 10.1186/1758-2946-2-s1-p12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Torrens F, Castellano G. Fullerite crystal thermodynamic characteristics and the law of corresponding states. JOURNAL OF NANOSCIENCE AND NANOTECHNOLOGY 2010; 10:1208-1222. [PMID: 20352780 DOI: 10.1166/jnn.2010.1858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The existence of single-wall carbon nanotubes in organic solvents in the form of clusters is discussed. A theory is developed based on a bundlet model, which enables describing the cluster-size distribution function. Comparison of calculated solubilities with experiments would permit obtaining energetic parameters, characterizing the interaction of a nanotube with its surrounding. Fullerenes and nanotubes are objects whose behaviour in many physical situations is characterized by peculiarities, which show up in that these systems represent the only soluble forms of carbon, what is related to their molecular structures. The fullerene molecule is a virtually uniform closed spherical-spheroidal surface and a nanotube is a smooth cylindrical unit. Both structures give rise to weak interactions between the neighbouring units in a crystal and promote their interaction with solvent molecules. The phenomena have a unified explanation in the bundlet model, in which the free energy of a nanotube in a cluster is combined from two components: a volume one proportional to the number of molecules n in a cluster and a surface one proportional to n1/2. Growth mechanisms of fractal clusters in fullerene solutions are analyzed along with similarity laws, determining the thermodynamic characteristics of fullerite crystals. In accordance with the similarity laws, the dimensionless Debye temperatures theta0 for all crystals belonging to the considered class should be close. Temperatures theta0 are determined by a similarity relation from experimental and estimated data. Fullerite theta0 is twice that for inert-gas crystals because, near the Debye point, the fullerite crystal is orientationally ordered so that its structure is dissimilar to face-centred cubic. A fullerene molecule whose thermal rotation is frozen cannot be considered as a spherically symmetric particle. The fulfilment of the similarity laws, which are valuable for particles with spherically symmetric interaction potential, would hardly be expected.
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Marrero-Ponce Y, Martínez-Albelo ER, Casañola-Martín GM, Castillo-Garit JA, Echevería-Díaz Y, Zaldivar VR, Tygat J, Borges JER, García-Domenech R, Torrens F, Pérez-Giménez F. Bond-based linear indices of the non-stochastic and stochastic edge-adjacency matrix. 1. Theory and modeling of ChemPhys properties of organic molecules. Mol Divers 2010; 14:731-53. [DOI: 10.1007/s11030-009-9201-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2009] [Accepted: 10/19/2009] [Indexed: 10/20/2022]
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Castillo-Garit J, Marrero-Ponce Y, Torrens F, García-Domenech R, Rodríguez-Borges J. Applications of Bond-Based 3D-Chiral Quadratic Indices in QSAR Studies Related to Central Chirality Codification. ACTA ACUST UNITED AC 2009. [DOI: 10.1002/qsar.200960085] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Torrens F, Castellano G. Topological Charge-Transfer Indices: From Small Molecules to Proteins. CURR PROTEOMICS 2009. [DOI: 10.2174/157016409789973770] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Castillo-Garit JA, Vega MC, Rolon M, Marrero-Ponce Y, Kouznetsov VV, Torres DFA, Gómez-Barrio A, Bello AA, Montero A, Torrens F, Pérez-Giménez F. Computational discovery of novel trypanosomicidal drug-like chemicals by using bond-based non-stochastic and stochastic quadratic maps and linear discriminant analysis. Eur J Pharm Sci 2009; 39:30-6. [PMID: 19854271 DOI: 10.1016/j.ejps.2009.10.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2009] [Revised: 10/01/2009] [Accepted: 10/13/2009] [Indexed: 11/28/2022]
Abstract
Herein we present results of a quantitative structure-activity relationship (QSAR) studies to classify and design, in a rational way, new antitrypanosomal compounds by using non-stochastic and stochastic bond-based quadratic indices. A data set of 440 organic chemicals, 143 with antitrypanosomal activity and 297 having other clinical uses, is used to develop QSAR models based on linear discriminant analysis (LDA). Non-stochastic model correctly classifies more than 93% and 95% of chemicals in both training and external prediction groups, respectively. On the other hand, the stochastic model shows an accuracy of about the 87% for both series. As an experiment of virtual lead generation, the present approach is finally satisfactorily applied to the virtual evaluation of 9 already synthesized in house compounds. The in vitro antitrypanosomal activity of this series against epimastigote forms of Trypanosoma cruzi is assayed. The model is able to predict correctly the behaviour for the majority of these compounds. Four compounds (FER16, FER32, FER33 and FER 132) showed more than 70% of epimastigote inhibition at a concentration of 100 microg/mL (86.74%, 78.12%, 88.85% and 72.10%, respectively) and two of these chemicals, FER16 (78.22% of AE) and FER33 (81.31% of AE), also showed good activity at a concentration of 10 microg/mL. At the same concentration, compound FER16 showed lower value of cytotoxicity (15.44%), and compound FER33 showed very low value of 1.37%. Taking into account all these results, we can say that these three compounds can be optimized in forthcoming works, but we consider that compound FER33 is the best candidate. Even though none of them resulted more active than Nifurtimox, the current results constitute a step forward in the search for efficient ways to discover new lead antitrypanosomals.
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Torrens F, Castellano G. Modelling of complex multicellular systems: tumour-immune cells competition. Chem Cent J 2009. [DOI: 10.1186/1752-153x-3-s1-p75] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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63
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Torrens F, Castellano G, Campos A, Abad C. Binding of water-soluble, globular proteins to anionic model membranes. J Mol Struct 2009. [DOI: 10.1016/j.molstruc.2008.12.040] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Castillo-Garit JA, Marrero-Ponce Y, Torrens F, García-Domenech R, Romero-Zaldivar V. Bond-based 3D-chiral linear indices: Theory and QSAR applications to central chirality codification. J Comput Chem 2008; 29:2500-12. [DOI: 10.1002/jcc.20964] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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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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Casañola-Martín GM, Marrero-Ponce Y, Tareq Hassan Khan M, Torrens F, Pérez-Giménez F, Rescigno A. Atom- and bond-based 2D TOMOCOMD-CARDD approach and ligand-based virtual screening for the drug discovery of new tyrosinase inhibitors. ACTA ACUST UNITED AC 2008; 13:1014-24. [PMID: 19015291 DOI: 10.1177/1087057108326078] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Two-dimensional atom- and bond-based TOMOCOMD-CARDD descriptors and linear discriminant analysis (LDA) are used in this report to perform a quantitative structure-activity relationship (QSAR) study of tyrosinase-inhibitory activity. A database of inhibitors of the enzyme is collected for this study, within 246 highly dissimilar molecules presenting antityrosinase activity. In total, 7 discriminant functions are obtained by using the whole set of atom- and bond-based 2D indices. All the LDA-based QSAR models show accuracies above 90% in the training set and values of the Matthews correlation coefficient (C) varying from 0.85 to 0.90. The external validation set shows globally good classifications between 89% and 91% and C values ranging from 0.75 to 0.81. Finally, QSAR models are used in the selection/identification of the 20 new dicoumarins subset to search for tyrosinase inhibitory activity. Theoretical and experimental results show good correspondence between one another. It is important to remark that most compounds in this series exhibit a more potent inhibitory activity against the mushroom tyrosinase enzyme than the reference compound, Kojic acid (IC(50) = 16.67 muM), resulting in a novel nucleus base (lead) with antityrosinase activity, and this could serve as a starting point for the drug discovery of novel tyrosinase inhibitor lead compounds. ( Journal of Biomolecular Screening 2008:1014-1024).
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Castillo-Garit JA, Martinez-Santiago O, Marrero-Ponce Y, Casañola-Martín GM, Torrens F. Atom-based non-stochastic and stochastic bilinear indices: Application to QSPR/QSAR studies of organic compounds. Chem Phys Lett 2008. [DOI: 10.1016/j.cplett.2008.08.094] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Castillo-Garit JA, Marrero-Ponce Y, Escobar J, Torrens F, Rotondo R. A novel approach to predict aquatic toxicity from molecular structure. CHEMOSPHERE 2008; 73:415-427. [PMID: 18597811 DOI: 10.1016/j.chemosphere.2008.05.024] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2008] [Revised: 04/29/2008] [Accepted: 05/07/2008] [Indexed: 05/26/2023]
Abstract
The main aim of the study was to develop quantitative structure-activity relationship (QSAR) models for the prediction of aquatic toxicity using atom-based non-stochastic and stochastic linear indices. The used dataset consist of 392 benzene derivatives, separated into training and test sets, for which toxicity data to the ciliate Tetrahymena pyriformis were available. Using multiple linear regression, two statistically significant QSAR models were obtained with non-stochastic (R2=0.791 and s=0.344) and stochastic (R2=0.799 and s=0.343) linear indices. A leave-one-out (LOO) cross-validation procedure was carried out achieving values of q2=0.781 (scv=0.348) and q2=0.786 (scv=0.350), respectively. In addition, a validation through an external test set was performed, which yields significant values of Rpred2 of 0.762 and 0.797. A brief study of the influence of the statistical outliers in QSAR's model development was also carried out. Finally, our method was compared with other approaches implemented in the Dragon software achieving better results. The non-stochastic and stochastic linear indices appear to provide an interesting alternative to costly and time-consuming experiments for determining toxicity.
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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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Torrens F, Gómez CM, León LM, Abad C, Campos A. Modeling Studies of the Phase Behavior of Monomer/Polymer/Disk Composites. MACROMOL THEOR SIMUL 2008. [DOI: 10.1002/mats.200800013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Torrens F, Castellano G. Fractal Dimension of Transdermal-Delivery Drug Models: 4-Alkylanilines. J LIQ CHROMATOGR R T 2008. [DOI: 10.1080/10826070802281877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Marrero-Ponce Y, Khan MTH, Casañola Martín GM, Ather A, Sultankhodzhaev MN, Torrens F, Rotondo R. Prediction of tyrosinase inhibition activity using atom-based bilinear indices. ChemMedChem 2008; 2:449-78. [PMID: 17366651 DOI: 10.1002/cmdc.200600186] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
A set of novel atom-based molecular fingerprints is proposed based on a bilinear map similar to that defined in linear algebra. These molecular descriptors (MDs) are proposed as a new means of molecular parametrization easily calculated from 2D molecular information. The nonstochastic and stochastic molecular indices match molecular structure provided by molecular topology by using the kth nonstochastic and stochastic graph-theoretical electronic-density matrices, M(k) and S(k), respectively. Thus, the kth nonstochastic and stochastic bilinear indices are calculated using M(k) and S(k) as matrix operators of bilinear transformations. Chemical information is coded by using different pair combinations of atomic weightings (mass, polarizability, vdW volume, and electronegativity). The results of QSAR studies of tyrosinase inhibitors using the new MDs and linear discriminant analysis (LDA) demonstrate the ability of the bilinear indices in testing biological properties. A database of 246 structurally diverse tyrosinase inhibitors was assembled. An inactive set of 412 drugs with other clinical uses was used; both active and inactive sets were processed by hierarchical and partitional cluster analyses to design training and predicting sets. Twelve LDA-based QSAR models were obtained, the first six using the nonstochastic total and local bilinear indices and the last six with the stochastic MDs. The discriminant models were applied; globally good classifications of 99.58 and 89.96 % were observed for the best nonstochastic and stochastic bilinear indices models in the training set along with high Matthews correlation coefficients (C) of 0.99 and 0.79, respectively, in the learning set. External prediction sets used to validate the models obtained were correctly classified, with accuracies of 100 and 87.78 %, respectively, yielding C values of 1.00 and 0.73. This subset contains 180 active and inactive compounds not considered to fit the models. A simulated virtual screen demonstrated this approach in searching tyrosinase inhibitors from compounds never considered in either training or predicting series. These fitted models permitted the selection of new cycloartane compounds isolated from herbal plants as new tyrosinase inhibitors. A good correspondence between theoretical and experimental inhibitory effects on tyrosinase was observed; compound CA6 (IC(50)=1.32 microM) showed higher activity than the reference compounds kojic acid (IC(50)=16.67 microM) and L-mimosine (IC(50)=3.68 microM).
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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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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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Torrens F, Castellano G. Improvement of charge-transfer indices for multifunctional amino acids: application to lysozyme. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2008; 19:643-654. [PMID: 19061081 DOI: 10.1080/10629360802551000] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Valence topological Charge-Transfer (CT) indices are applied to the calculation of pH at the isoelectric point (pI). The model is generalized for molecules with heteroatoms. The ability of the indices for the description of molecular charge distribution is established by comparing them with the pI of 21 amino acids. Linear correlation models are obtained. The CT indices improve multivariable regression equations for pI. The variance decreases by 95%. No superimposition of the corresponding G(k)-J(k) and G(k)(V)-J(k)(V) pairs is observed in most fits, which diminishes the risk of collinearity. The inclusion of heteroatoms in pi-electron system is beneficial for the description of pI, the because of either the role of the additional p orbitals provided by heteroatom or the role of steric factors in pi-electron conjugation. The use of CT/valence CT indices {G(k), J(k), G(k)(V), J(k)(V)} gives limited results for modelling amino acid pI. The inclusion of the number of acidic/basic groups improves the models. The effect is specially noticeable for amino acids with more than two functional groups. The fitting line for 21 amino acids is used to estimate lysozyme pI replacing (1 + Delta n/n(T)) with (M + Delta n)/n(T). The results for lysozyme fragments can estimate the pI of the whole protein with 1-13% error.
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