1
|
Hawe GI, Alkorta I, Popelier PLA. Prediction of the Basicities of Pyridines in the Gas Phase and in Aqueous Solution. J Chem Inf Model 2010; 50:87-96. [DOI: 10.1021/ci900396k] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Glenn I. Hawe
- Manchester Interdisciplinary Biocentre (MIB), 131 Princess Street, Manchester M1 7DN, Great Britain, and School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, Great Britain, Instituto de Química Médica (CSIC), Juan de la Cierva 3, 28006-Madrid, Spain
| | - Ibon Alkorta
- Manchester Interdisciplinary Biocentre (MIB), 131 Princess Street, Manchester M1 7DN, Great Britain, and School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, Great Britain, Instituto de Química Médica (CSIC), Juan de la Cierva 3, 28006-Madrid, Spain
| | - Paul L. A. Popelier
- Manchester Interdisciplinary Biocentre (MIB), 131 Princess Street, Manchester M1 7DN, Great Britain, and School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, Great Britain, Instituto de Química Médica (CSIC), Juan de la Cierva 3, 28006-Madrid, Spain
| |
Collapse
|
2
|
Xue C, Popelier PLA. Prediction of interaction energies of substituted hydrogen-bonded Watson-Crick cytosine:guanine(8X) base pairs. J Phys Chem B 2009; 113:3245-50. [PMID: 19260717 DOI: 10.1021/jp8071926] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We investigated the variation in the interaction energy between the Watson-Crick hydrogen-bonded DNA base pairs guanine and cytosine (G(8X):C), where guanine is substituted in the C8 position by 37 different functional groups. Base pairs were optimized at the B3LYP/6-311+G(2d,p) level. A base pair complex containing a more strongly electron-withdrawing group remarkably forms a more stable base pair with C. Multivariate linear regression provided a quantitative relationship between the interaction energies and descriptors generated by the quantum chemical topology (QCT) approach. The descriptors were sampled from the monomers only, not the supermolecular base pair complexes. A model with r2 = 0.96 and a root-mean-square (rms) value of 0.6 kJ/mol was obtained for a training set of 28 base pair complexes. The model was tested by an external test set of 9 complexes, yielding r2 = 0.99 and an rms value of 0.2 kJ/mol. The results indicated that the bonds C6=O6 and N2-H2 at the hydrogen-bonded frontier of the guanine derivatives play an important role in transmitting the substituent effects. A linear correlation between substitution energies and Hammett constants (sigma(m)) was also obtained for all 37 substituents, yielding r2 = 0.82 and an rms value of 1.2 kJ/mol. The model based on QCT descriptors can therefore be used for the prediction of the interaction energy of the base pair G(8x):C, strictly based on data for the G(8x) monomers only.
Collapse
Affiliation(s)
- Chunxia Xue
- Manchester Interdisciplinary Biocentre (MIB), 131 Princess Street, Manchester M1 7DN, Great Britain
| | | |
Collapse
|
3
|
Carbó-Dorca R, Gallegos A, Sánchez ÁJ. Notes on quantitative structure-properties relationships (QSPR) (1): A discussion on a QSPR dimensionality paradox (QSPR DP) and its quantum resolution. J Comput Chem 2009; 30:1146-59. [DOI: 10.1002/jcc.21145] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
4
|
Roy K, Popelier PLA. Predictive QSPR modeling of the acidic dissociation constant (pKa) of phenols in different solvents. J PHYS ORG CHEM 2009. [DOI: 10.1002/poc.1447] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
5
|
Hemmateenejad B, Mehdipour AR, Popelier PLA. Quantum Topological QSAR Models based on the MOLMAP Approach. Chem Biol Drug Des 2008; 72:551-63. [DOI: 10.1111/j.1747-0285.2008.00731.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
6
|
Roy K, Popelier P. Exploring Predictive QSAR Models Using Quantum Topological Molecular Similarity (QTMS) Descriptors for Toxicity of Nitroaromatics toSaccharomyces cerevisiae. ACTA ACUST UNITED AC 2008. [DOI: 10.1002/qsar.200810028] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
7
|
Mohajeri A, Dinpajooh M. Structure–toxicity relationship for aliphatic compounds using quantum topological descriptors. ACTA ACUST UNITED AC 2008. [DOI: 10.1016/j.theochem.2007.12.037] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
8
|
Xue C, Popelier PLA. Computational Study of Substituent Effects on the Interaction Energies of Hydrogen-Bonded Watson−Crick Cytosine:Guanine Base Pairs. J Phys Chem B 2008; 112:5257-64. [DOI: 10.1021/jp7108913] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Chunxia Xue
- Manchester Interdisciplinary Biocentre (MIB), 131 Princess Street, Manchester, M1 7DN, Great Britain
| | - Paul L. A. Popelier
- Manchester Interdisciplinary Biocentre (MIB), 131 Princess Street, Manchester, M1 7DN, Great Britain
| |
Collapse
|
9
|
Bytheway I, Darley M, Popelier P. The Calculation of Polar Surface Area from First Principles: An Application of Quantum Chemical Topology to Drug Design. ChemMedChem 2008; 3:445-53. [DOI: 10.1002/cmdc.200700262] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
10
|
Singh N, Loader RJ, O'Malley PJ, Popelier PLA. Computation of relative bond dissociation enthalpies (DeltaBDE) of phenolic antioxidants from quantum topological molecular similarity (QTMS). J Phys Chem A 2007; 110:6498-503. [PMID: 16706407 DOI: 10.1021/jp0553885] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A recently proposed method called quantitative topological molecular similarity (QTMS) generated a model for the computation of the relative substituent effects on the bond dissociation enthalpies (DeltaBDEs) for a set of 39 phenols. The data set includes a diverse set of substituents with monosubstituted and poly-substituted derivatives that exhibit different electronic and steric effects. Many share common structural features with already well-established antioxidants. QTMS reveals the active region of the substituted phenols and identifies the electronic descriptors that best explain the range of DeltaBDEs observed. For substituents in the 4-X position (para) we find that our model requires a correction for radical stabilization enthalpy (RSE). Application of the QTMS methodology yields an unrivalled QSAR with r(2) = 0.98 and q(2) = 0.85 for the bond dissociation enthalpies of this phenolic antioxidant data set.
Collapse
Affiliation(s)
- Nakul Singh
- School of Chemistry, The University of Manchester, Manchester M60 1QD, UK
| | | | | | | |
Collapse
|
11
|
Buttingsrud B, Alsberg BK, Astrand PO. Validation of critical points in the electron density as descriptors by building quantitative structure-property relationships for the atomic polar tensor. J Comput Chem 2007; 28:2130-9. [PMID: 17464968 DOI: 10.1002/jcc.20666] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
A crucial component of research in the field of quantitative structure-activity/property relationships is the identification of molecular descriptors relevant to the activity or property of interest. Descriptors based on the topology of the electron density as formulated in Bader's theory of atoms in molecules are investigated in detail in this work. In a model study, the authors investigate their ability to predict the atomic polar tensor (the gradient of the molecular dipole moment), which contains information on the vibrational intensities in infrared spectroscopy and constitutes a scheme for partitioning the total charge distribution into atomic charges. The atomic polar tensor may therefore be used to investigate whether the descriptors give adequate information on the local electronic structure in the molecule. Both the trace of the atomic polar tensor and for planar molecules its out-of-plane component may be interpreted as definitions of atomic charges suitable for prediction. Hydrogen and carbon atoms in a set of 60 aromatic compounds with various substituents have been studied. Excellent results for prediction of hydrogen and carbon charges have been achieved with cross-validated squared correlation coefficients between predicted and theoretical values varying from 0.92 and 0.977 for the most complex set of substituents when the value, Laplacian, and ellipticity of the electron density in the bond critical points are used as descriptors. The carbon charges defined from the trace of the atomic polar tensor are correlated with its out-of-plane component whereas such relationship is not observed for the hydrogen charges studied in this work.
Collapse
Affiliation(s)
- Bård Buttingsrud
- Department of Chemistry, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
| | | | | |
Collapse
|
12
|
Hukka TI, Pakkanen TT. Modeling the Interaction between Two- and Four-Ring Progestin Models and a Silicone-Based Polymer Model: A Density Functional Theory Study. J Chem Inf Model 2007; 47:535-46. [PMID: 17381171 DOI: 10.1021/ci6002625] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this paper, we introduce a relatively fast and reliable method for determining the feasibility of drug delivery from transdermal and implant materials. We are using density functional theory for modeling the interaction of progestins, that is, progesterone and six of its hydroxyl derivatives, with a silicone-based polymer. The silicone-based polymer model is a linear molecule, which consists of four dimethylsiloxane units. The progestin models are (1) complete progestin structures, which are called four-ring models, and (2) their two-ring models, which are comprised of the C and D rings of the basic steroid skeletons. We are investigating the interaction between the four- and two-ring models and the polymer model in three different interaction configurations. Altogether, 42 different equilibrium geometries of progestin-polymer model complexes and the corresponding interaction energies have been calculated. Our computational results are in very good agreement with the experimental findings reported previously in the literature, which state that the release rates and permeabilities of progestin pharmaceuticals in silicone-based drug delivery systems decrease when the number of hydroxyl groups is increased in the steroid skeleton. The four-ring models take the total interaction of the steroid into account slightly better than the two-ring models. However, the two-ring models are very good for predicting the local interactions between the steroid and the polymer model.
Collapse
Affiliation(s)
- Terttu I Hukka
- Institute of Materials Chemistry, Tampere University of Technology, P.O. Box 541, 33101 Tampere, Finland.
| | | |
Collapse
|
13
|
Chapter 15 A quantitative structure-activity relationship of 1,4-dihydropyridine calcium channel blockers with electronic descriptors produced by quantum chemical topology. ACTA ACUST UNITED AC 2007. [DOI: 10.1016/s1380-7323(07)80016-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
|
14
|
Buttingsrud B, Ryeng E, King RD, Alsberg BK. Representation of molecular structure using quantum topology with inductive logic programming in structure-activity relationships. J Comput Aided Mol Des 2006; 20:361-73. [PMID: 17054018 DOI: 10.1007/s10822-006-9058-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2006] [Accepted: 07/20/2006] [Indexed: 10/24/2022]
Abstract
The requirement of aligning each individual molecule in a data set severely limits the type of molecules which can be analysed with traditional structure activity relationship (SAR) methods. A method which solves this problem by using relations between objects is inductive logic programming (ILP). Another advantage of this methodology is its ability to include background knowledge as 1st-order logic. However, previous molecular ILP representations have not been effective in describing the electronic structure of molecules. We present a more unified and comprehensive representation based on Richard Bader's quantum topological atoms in molecules (AIM) theory where critical points in the electron density are connected through a network. AIM theory provides a wealth of chemical information about individual atoms and their bond connections enabling a more flexible and chemically relevant representation. To obtain even more relevant rules with higher coverage, we apply manual postprocessing and interpretation of ILP rules. We have tested the usefulness of the new representation in SAR modelling on classifying compounds of low/high mutagenicity and on a set of factor Xa inhibitors of high and low affinity.
Collapse
Affiliation(s)
- Bård Buttingsrud
- Chemometrics and Bioinformatics Group, Department of chemistry, Norwegian University of Science and Technology, Trondheim, Norway
| | | | | | | |
Collapse
|
15
|
Popelier PLA, Smith PJ. QSAR models based on quantum topological molecular similarity. Eur J Med Chem 2006; 41:862-73. [PMID: 16697489 DOI: 10.1016/j.ejmech.2006.03.004] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 03/01/2006] [Accepted: 03/20/2006] [Indexed: 12/01/2022]
Abstract
A new method called quantum topological molecular similarity (QTMS) was fairly recently proposed [J. Chem. Inf. Comp. Sc., 41, 2001, 764] to construct a variety of medicinal, ecological and physical organic QSAR/QSPRs. QTMS method uses quantum chemical topology (QCT) to define electronic descriptors drawn from modern ab initio wave functions of geometry-optimised molecules. It was shown that the current abundance of computing power can be utilised to inject realistic descriptors into QSAR/QSPRs. In this article we study seven datasets of medicinal interest : the dissociation constants (pK(a)) for a set of substituted imidazolines , the pK(a) of imidazoles , the ability of a set of indole derivatives to displace [(3)H] flunitrazepam from binding to bovine cortical membranes , the influenza inhibition constants for a set of benzimidazoles , the interaction constants for a set of amides and the enzyme liver alcohol dehydrogenase , the natriuretic activity of sulphonamide carbonic anhydrase inhibitors and the toxicity of a series of benzyl alcohols. A partial least square analysis in conjunction with a genetic algorithm delivered excellent models. They are also able to highlight the active site, of the ligand or the molecule whose structure determines the activity. The advantages and limitations of QTMS are discussed.
Collapse
Affiliation(s)
- P L A Popelier
- School of Chemistry, Sackville Site, North Campus, University of Manchester, UK.
| | | |
Collapse
|
16
|
Loader RJ, Singh N, O'malley PJ, Popelier PLA. The cytotoxicity of ortho alkyl substituted 4-X-phenols: A QSAR based on theoretical bond lengths and electron densities. Bioorg Med Chem Lett 2006; 16:1249-54. [PMID: 16338238 DOI: 10.1016/j.bmcl.2005.11.079] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2005] [Revised: 11/18/2005] [Accepted: 11/19/2005] [Indexed: 11/24/2022]
Abstract
A new method called quantum topological molecular similarity (QTMS) was recently proposed [O'Brien, S. E.; Popelier, P. L. A. J. Chem. Inf. Comp. Sci.2001, 41, 764] and has been shown to be successful in a variety of medicinal, ecological and physical organic QSAR/QSPRs. QTMS method uses electronic descriptors drawn from ab initio wavefunctions of geometry-optimized molecules. We investigated a remarkable and unusual set of ortho alkyl-substituted phenols [Selassie, C. D.; Verma, R. P.; Kapur, S.; Shusterman, A. J.; Hansch, C. J. Chem. Soc., Perkin2002, II, 1112], recently studied by the Hansch group. Our results do not support their proposal that a steric factor is important in the determination of the cytotoxicity of this set of substituted phenols. Thus, we conclude that the cytotoxicity of these sterically encumbered phenols is dependent primarily on electronic and radical effects, and that steric issues do not appear to be a critical distinguishing factor.
Collapse
Affiliation(s)
- R J Loader
- School of Chemistry, Sackville Site, University of Manchester, Manchester M60 1QD, UK
| | | | | | | |
Collapse
|
17
|
Popelier PLA, Smith PJ, Chaudry UA. Quantitative structure-activity relationships of mutagenic activity from quantum topological descriptors: triazenes and halogenated hydroxyfuranones (mutagen-X) derivatives. J Comput Aided Mol Des 2005; 18:709-18. [PMID: 15865063 DOI: 10.1007/s10822-004-6815-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The mutagenic activity of 23 triazenes and, in a different set, of 24 halogenated hydroxyfuranones (MX derivatives) is quantitatively related to new features of contemporary molecular wave functions. Nowadays affordable computers are powerful enough to rapidly generate geometry-optimised ab initio wave functions at HF/3-21G*, HF/6-31G* and B3LYP/6-311 + G(2d,p) level for all molecules. The bonds of a common molecular skeleton are described by their ab initio bond lengths and local properties provided by the theory of quantum chemical topology (QCT). The chemometric analysis involves two types: one to generate a statistically validated quantitative model, and one to isolate the active center. In the former a genetic algorithm (GA) selects bond descriptors in order to optimise the cross-validation error, q2, followed by a full partial least squares (PLS) analysis, which also yields randomisation statistics. In the latter type principal components (PCs) are constructed from the original bond descriptors and their variables important to the projection (VIPs) are plotted in a histogram. This analysis suggests a preferred mechanistic pathway for the initial hydroxylation of the triazenes, an issue that has remained ambiguous so far. In the case of the hydroxyfuranones the proposed method aids the elucidation of a mechanistic ambivalence.
Collapse
Affiliation(s)
- P L A Popelier
- School of Chemistry, University of Manchester, Manchester M60 1QD, UK.
| | | | | |
Collapse
|
18
|
Smith PJ, Popelier PLA. Quantum chemical topology (QCT) descriptors as substitutes for appropriate Hammett constants. Org Biomol Chem 2005; 3:3399-407. [PMID: 16132102 DOI: 10.1039/b507024d] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A technique called quantum topological molecular similarity (QTMS) was recently proposed [J. Chem. Inf. Comput. Sci., 2001, 41, 764] in order to construct a variety of medicinal, ecological and physical organic QSAR/QSPRs, based on modern ab initio wave functions of geometry optimised molecules, in combination with quantum chemical topology (QCT). The current abundance of computing power can be utilised to inject realistic descriptors into QSAR/QSPRs. In previous work [J. Chem. Soc., Perkin Trans. 2, 2002, 1231] it was proven that a set of Hammett constants (sigma(p), sigma(m), sigma(I) and sigma(p)0) for a sizeable set of mono- and polysubstituted carboxylic acids can be replaced by QCT bond descriptors. Using QTMS and proper statistical validation we examined seven data sets in total. The first three sets (para-substituted phenols (sigma-), substituted toluenes (sigma+) and bromophenethylamines (sigma+)) corroborate that a wider class of Hammett constants can also be replaced by QCT descriptors. A fourth set (benzyl radicals) focuses on non-Hammett behaviour being superimposed on Hammett behaviour. QCT descriptors selectively correlate with Hammett behaviour. The QTMS analysis of the last three sets (toxicity of benzyl alcohols, chromatographic capacity factors of chalcones and herbicidal activity of 5-chloro-2,3-dicyanopyrazines) screens for false positives. This test is successfully passed in that QCT descriptors fail when lipophilicity/hydrophobicity is in charge. Hence, overall, the discriminatory capacity of QCT descriptors is established, in detecting Hammett behaviour and specifically replacing the Hammett constants by more modern and non-empirical descriptors.
Collapse
Affiliation(s)
- P J Smith
- School of Chemistry, Faraday Building, Sackville Site, University of Manchester, Manchester, M60 1QD, Great Britain
| | | |
Collapse
|