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García-Jacas CR, Marrero-Ponce Y, Hernández-Ortega T, Martinez-Mayorga K, Cabrera-Leyva L, Ledesma-Romero JC, Aguilera-Fernández I, Rodríguez-León AR. Tensor algebra-based geometric methodology to codify central chirality on organic molecules. SAR QSAR Environ Res 2017; 28:541-556. [PMID: 28705027 DOI: 10.1080/1062936x.2017.1344729] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 06/16/2017] [Indexed: 06/07/2023]
Abstract
A novel mathematical procedure to codify chiral features of organic molecules in the QuBiLS-MIDAS framework is introduced. This procedure constitutes a generalization to that commonly used to date, where the values 1 and -1 (correction factor) are employed to weight the molecular vectors when each atom is labelled as R (rectus) or S (sinister) according to the Cahn-Ingold-Prelog rules. Therefore, values in the range [Formula: see text] with steps equal to 0.25 may be accounted for. The atoms labelled R or S can have negative and positive values assigned (e.g. -3 for an R atom and 1 for an S atom, or vice versa), opposed values (e.g. -3 for an R atom and 3 for an S atom, or vice versa), positive values (e.g. 3 for an R atom and 1 for an S atom) or negative values (e.g. -3 for an R atom and -1 for an S atom). These proposed Chiral QuBiLS-MIDAS 3D-MDs are real numbers, non-symmetric and reduced to 'classical' (non-chiral) QuBiLS-MIDAS 3D-MDs when symmetry is not codified (correction factor equal to zero). In this report, only the factors with opposed values were considered with the purpose of demonstrating the feasibility of this proposal. From QSAR modelling carried out on four chemical datasets (Cramer's steroids, fenoterol stereoisomer derivatives, N-alkylated 3-(3-hydroxyphenyl)-piperidines, and perindoprilat stereoisomers), it was demonstrated that the use of several correction factors contributes to the building of models with greater robustness and predictive ability than those reported in the literature, as well as with respect to the models exclusively developed with QuBiLS-MIDAS 3D-MDs based on the factor 1 | -1. In conclusion, it can be stated that this novel strategy constitutes a suitable alternative to computed chirality-based descriptors, contributing to the development of good models to predict properties depending on symmetry.
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Affiliation(s)
- C R García-Jacas
- a Instituto de Química, Universidad Nacional Autónoma de México (UNAM) , Ciudad de México , México
- b Escuela de Sistemas y Computación , Pontificia Universidad Católica del Ecuador Sede Esmeraldas (PUCESE) , Esmeraldas , Ecuador
- g Grupo de Investigación de Bioinformática , Universidad de las Ciencias Informáticas (UCI) , La Habana , Cuba
| | - Y Marrero-Ponce
- c Computer-Aided Molecular "Biosilico" Discovery and Bioinformatics Research International Network (CAMD-BIR IN) , Quito , Ecuador
- d Universidad San Francisco de Quito (USFQ), Grupo de Medicina Molecular y Traslacional (MeM&T), Colegio de Ciencias de la Salud (COCSA), Escuela de Medicina , Quito , Pichincha , Ecuador
- e Universidad San Francisco de Quito (USFQ), Instituto de Simulación Computacional (ISC-USFQ) , Quito , Pichincha , Ecuador
- f Grupo de Investigación Ambiental (GIA) , Programas Ambientales, Facultad de Ingenierías, Fundación Universitaria Tecnológico de Comfenalco (COMFENALCO) , Cartagena de Indias , Bolívar , Colombia
| | - T Hernández-Ortega
- g Grupo de Investigación de Bioinformática , Universidad de las Ciencias Informáticas (UCI) , La Habana , Cuba
| | - K Martinez-Mayorga
- a Instituto de Química, Universidad Nacional Autónoma de México (UNAM) , Ciudad de México , México
| | - L Cabrera-Leyva
- h Grupo de Investigación de Inteligencia Artificial (AIRES), Facultad de Informática , Universidad de Camagüey , Camagüey , Cuba
| | - J C Ledesma-Romero
- g Grupo de Investigación de Bioinformática , Universidad de las Ciencias Informáticas (UCI) , La Habana , Cuba
| | - I Aguilera-Fernández
- g Grupo de Investigación de Bioinformática , Universidad de las Ciencias Informáticas (UCI) , La Habana , Cuba
| | - A R Rodríguez-León
- g Grupo de Investigación de Bioinformática , Universidad de las Ciencias Informáticas (UCI) , La Habana , Cuba
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García-Jacas CR, Marrero-Ponce Y, Barigye SJ, Hernández-Ortega T, Cabrera-Leyva L, Fernández-Castillo A. N-tuple topological/geometric cutoffs for 3D N-linear algebraic molecular codifications: variability, linear independence and QSAR analysis. SAR QSAR Environ Res 2016; 27:949-975. [PMID: 27707004 DOI: 10.1080/1062936x.2016.1231714] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 08/30/2016] [Indexed: 06/06/2023]
Abstract
Novel N-tuple topological/geometric cutoffs to consider specific inter-atomic relations in the QuBiLS-MIDAS framework are introduced in this manuscript. These molecular cutoffs permit the taking into account of relations between more than two atoms by using (dis-)similarity multi-metrics and the concepts related with topological and Euclidean-geometric distances. To this end, the kth two-, three- and four-tuple topological and geometric neighbourhood quotient (NQ) total (or local-fragment) spatial-(dis)similarity matrices are defined, to represent 3D information corresponding to the relations between two, three and four atoms of the molecular structures that satisfy certain cutoff criteria. First, an analysis of a diverse chemical space for the most common values of topological/Euclidean-geometric distances, bond/dihedral angles, triangle/quadrilateral perimeters, triangle area and volume was performed in order to determine the intervals to take into account in the cutoff procedures. A variability analysis based on Shannon's entropy reveals that better distribution patterns are attained with the descriptors based on the cutoffs proposed (QuBiLS-MIDAS NQ-MDs) with regard to the results obtained when all inter-atomic relations are considered (QuBiLS-MIDAS KA-MDs - 'Keep All'). A principal component analysis shows that the novel molecular cutoffs codify chemical information captured by the respective QuBiLS-MIDAS KA-MDs, as well as information not captured by the latter. Lastly, a QSAR study to obtain deeper knowledge of the contribution of the proposed methods was carried out, using four molecular datasets (steroids (STER), angiotensin converting enzyme (ACE), thermolysin inhibitors (THER) and thrombin inhibitors (THR)) widely used as benchmarks in the evaluation of several methodologies. One to four variable QSAR models based on multiple linear regression were developed for each compound dataset following the original division into training and test sets. The results obtained reveal that the novel cutoff procedures yield superior performances relative to those of the QuBiLS-MIDAS KA-MDs in the prediction of the biological activities considered. From the results achieved, it can be suggested that the proposed N-tuple topological/geometric cutoffs constitute a relevant criteria for generating MDs codifying particular atomic relations, ultimately useful in enhancing the modelling capacity of the QuBiLS-MIDAS 3D-MDs.
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Affiliation(s)
- C R García-Jacas
- a Escuela de Sistemas y Computación , Pontificia Universidad Católica del Ecuador Sede Esmeraldas (PUCESE) , Esmeraldas , Ecuador
- b Grupo de Investigación de Bioinformática , Instituto de Química, Universidad Nacional Autónoma de México (UNAM) , Ciudad de México , D.F, México
- c Grupo de Investigacion de Bioinformatica , Universidad de las Ciencias Informaticas (UCI) , La Habana , Cuba
| | - Y Marrero-Ponce
- d Grupo de Medicina Molecular y Traslacional (MeM&T) , Universidad San Francisco de Quito (USFQ) , Quito , Ecuador
- e Instituto de Simulación Computacional (ISC-USFQ), Universidad San Francisco de Quito (USFQ) , Quito , Ecuador
| | - S J Barigye
- g Department of Chemistry , McGill University , Montréal , Québec , Canada
| | - T Hernández-Ortega
- c Grupo de Investigacion de Bioinformatica , Universidad de las Ciencias Informaticas (UCI) , La Habana , Cuba
| | - L Cabrera-Leyva
- f Grupo de Investigación de Inteligencia Artificial (AIRES) , Universidad de Camagüey , Camagüey , Cuba
| | - A Fernández-Castillo
- c Grupo de Investigacion de Bioinformatica , Universidad de las Ciencias Informaticas (UCI) , La Habana , Cuba
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