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Topological Indices of Hyaluronic Acid-Paclitaxel Conjugates’ Molecular Structure in Cancer Treatment. OPEN CHEM 2019. [DOI: 10.1515/chem-2019-0009] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
AbstractA large number of medical experiments have confirmed that the features of drugs have a close correlation with their molecular structure. Drug properties can be obtained by studying the molecular structure of corresponding drugs. The calculation of the topological index of a drug structure enables scientists to have a better understanding of the physical chemistry and biological characteristics of drugs. In this paper, we focus on Hyaluronic Acid-Paclitaxel conjugates which are widely used in the manufacture of anticancer drugs. Several topological indices are determined by virtue of the edge-partition method, and our results remedy the lack of medicine experiments, thus providing a theoretical basis for pharmaceutical engineering.
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Abstract
Descriptors are one of the most essential components of predictive Quantitative Structure-Activity/Property/Toxicity Relationship (QSAR/QSPR/QSTR) modeling analysis, as they encode chemical information of molecules in the form of quantitative numbers, which are used to develop mathematical correlation models. The quality of a predictive model not only depends on good modeling statistics, but also on the extraction of chemical features. A significant amount of research since the beginning of QSAR analysis paradigm has led to the introduction of a large number of predictor variables or descriptors. The Extended Topochemical Atom (ETA) indices, developed by the authors' group, successfully address the aspects of molecular topology, electronic information, and different types of bonded interactions, and have been extensively employed for the modeling of different types of activity/property and toxicity endpoints. This chapter provides explicit information regarding the basis, algorithm, and applicability of the ETA indices for a predictive modeling paradigm.
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Barigye SJ, Marrero-Ponce Y, Zupan J, Pérez-Giménez F, Freitas MP. Structural and Physicochemical Interpretation of GT-STAF Information Theory-Based Indices. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2015. [DOI: 10.1246/bcsj.20140037] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Stephen J. Barigye
- Departamento de Química, Universidade Federal de Lavras, UFLA
- Unit of Computer-Aided Molecular “Biosilico” Discovery and Bioinformatic Research (CAMD-BIR Unit), Faculty of Chemistry-Pharmacy, Universidad Central “Martha Abreu” de Las Villas
| | - Yovani Marrero-Ponce
- Unit of Computer-Aided Molecular “Biosilico” Discovery and Bioinformatic Research (CAMD-BIR Unit), Faculty of Chemistry-Pharmacy, Universidad Central “Martha Abreu” de Las Villas
- Institut Universitari de Ciència Molecular, Universitat de València, Edifici d’Instituts de Paterna
- Unidad de Investigación de Diseño de Fármacos y Conectividad Molecular, Departamento de Química Física, Facultad de Farmacia, Universitat de València
- Facultad de Química Farmacéutica, Universidad de Cartagena
| | - Jure Zupan
- Laboratory of Chemometrics, National Institute of Chemistry
| | - Facundo Pérez-Giménez
- Unidad de Investigación de Diseño de Fármacos y Conectividad Molecular, Departamento de Química Física, Facultad de Farmacia, Universitat de València
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Roy K, Das RN. The “ETA” Indices in QSAR/QSPR/QSTR Research. QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIPS IN DRUG DESIGN, PREDICTIVE TOXICOLOGY, AND RISK ASSESSMENT 2015. [DOI: 10.4018/978-1-4666-8136-1.ch002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Descriptors are one of the most essential components of predictive Quantitative Structure-Activity/Property/Toxicity Relationship (QSAR/QSPR/QSTR) modeling analysis, as they encode chemical information of molecules in the form of quantitative numbers, which are used to develop mathematical correlation models. The quality of a predictive model not only depends on good modeling statistics, but also on the extraction of chemical features. A significant amount of research since the beginning of QSAR analysis paradigm has led to the introduction of a large number of predictor variables or descriptors. The Extended Topochemical Atom (ETA) indices, developed by the authors' group, successfully address the aspects of molecular topology, electronic information, and different types of bonded interactions, and have been extensively employed for the modeling of different types of activity/property and toxicity endpoints. This chapter provides explicit information regarding the basis, algorithm, and applicability of the ETA indices for a predictive modeling paradigm.
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Derivatives in discrete mathematics: a novel graph-theoretical invariant for generating new 2/3D molecular descriptors. I. Theory and QSPR application. J Comput Aided Mol Des 2012; 26:1229-46. [DOI: 10.1007/s10822-012-9591-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2012] [Accepted: 07/19/2012] [Indexed: 10/27/2022]
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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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Milic̆ević A, Raos N. Estimation of Stability Constants of Copper(II) Complexes with α-Amino Acids Using Connectivity Index 3χv. Common Model for the Binary and Ternary Complexes. CHINESE J CHEM 2011. [DOI: 10.1002/cjoc.201180316] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Pogliani L. Model of twelve properties of a set of organic solvents with graph-theoretical and/or experimental parameters. J Comput Chem 2010; 31:295-307. [PMID: 19462460 DOI: 10.1002/jcc.21319] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Twelve properties of a highly heterogeneous class of organic solvents have been modeled with a graph-theoretical molecular connectivity modified (MC) method, which allows to encode the core electrons and the hydrogen atoms. The graph-theoretical method uses the concepts of simple, general, and complete graphs, where these last types of graphs are used to encode the core electrons. The hydrogen atoms have been encoded by the aid of a graph-theoretical perturbation parameter, which contributes to the definition of the valence delta, delta(v), a key parameter in molecular connectivity studies. The model of the twelve properties done with a stepwise search algorithm is always satisfactory, and it allows to check the influence of the hydrogen content of the solvent molecules on the choice of the type of descriptor. A similar argument holds for the influence of the halogen atoms on the type of core electron representation. In some cases the molar mass, and in a minor way, special "ad hoc" parameters have been used to improve the model. A very good model of the surface tension could be obtained by the aid of five experimental parameters. A mixed model method based on experimental parameters plus molecular connectivity indices achieved, instead, to consistently improve the model quality of five properties. To underline is the importance of the boiling point temperatures as descriptors in these last two model methodologies.
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Affiliation(s)
- Lionello Pogliani
- Dipartimento di Chimica, Università della Calabria, via P. Bucci, 14 C, 87036 Rende, Italy.
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Design of novel antituberculosis compounds using graph-theoretical and substructural approaches. Mol Divers 2009; 13:445-58. [PMID: 19340599 DOI: 10.1007/s11030-009-9129-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2008] [Accepted: 02/16/2009] [Indexed: 10/20/2022]
Abstract
The increasing resistance of Mycobacterium tuberculosis to the existing drugs has alarmed the worldwide scientific community. In an attempt to overcome this problem, two models for the design and prediction of new antituberculosis agents were obtained. The first used a mixed approach, containing descriptors based on fragments and the topological substructural molecular design approach (TOPS-MODE) descriptors. The other model used a combination of two-dimensional (2D) and three-dimensional (3D) descriptors. A data set of 167 compounds with great structural variability, 72 of them antituberculosis agents and 95 compounds belonging to other pharmaceutical categories, was analyzed. The first model showed sensitivity, specificity, and accuracy values above 80% and the second one showed values higher than 75% for these statistical indices. Subsequently, 12 structures of imidazoles not included in this study were designed, taking into account the two models. In both cases accuracy was 100%, showing that the methodology in silico developed by us is promising for the rational design of antituberculosis drugs.
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Chen J, Hundertmark D, Martínez TJ. A unified theoretical framework for fluctuating-charge models in atom-space and in bond-space. J Chem Phys 2008; 129:214113. [DOI: 10.1063/1.3021400] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
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Miličević A, Raos N. Influence of Chelate Ring Interactions on Copper(II) Chelate Stability Studied by Connectivity Index Functions. J Phys Chem A 2008; 112:7745-9. [DOI: 10.1021/jp802018m] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ante Miličević
- Institute for Medical Research and Occupational Health, Ksaverska c. 2, P.O. Box 291, HR-10000 Zagreb, Croatia
| | - Nenad Raos
- Institute for Medical Research and Occupational Health, Ksaverska c. 2, P.O. Box 291, HR-10000 Zagreb, Croatia
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García-Domenech R, Galvez J, de Julian-Ortiz JV, Pogliani L. Some new trends in chemical graph theory. Chem Rev 2008; 108:1127-69. [PMID: 18302420 DOI: 10.1021/cr0780006] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ramón García-Domenech
- Unidad de Investigación de Diseño de Farmacos y Conectividad Molecular, Departamento de Química Fisica, Facultad de Farmacía, Universitat de València, 46100 Burjassot, València, Spain
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Taherpour A(A, Shafiei F. The structural relationship between Randić indices, adjacency matrixes, distance matrixes and maximum wave length of linear simple conjugated polyene compounds. ACTA ACUST UNITED AC 2005. [DOI: 10.1016/j.theochem.2005.03.053] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Pogliani L. Complete graph conjecture for inner-core electrons: homogeneous index case. J Comput Chem 2003; 24:1097-109. [PMID: 12759909 DOI: 10.1002/jcc.10277] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The complete graph conjecture that encodes the inner-core electrons of atoms with principal quantum number n >or= 2 with complete graphs, and especially with odd complete graphs, is discussed. This conjecture is used to derive new values for the molecular connectivity and pseudoconnectivity basis indices of hydrogen-suppressed chemical pseudographs. For atoms with n = 2 the new values derived with this conjecture are coincident with the old ones. The modeling ability of the new homogeneous basis indices, and of the higher-order terms, is tested and compared with previous modeling studies, which are centered on basis indices that are either based on quantum concepts or partially based on this new conjecture for the inner-core electrons. Two similar algorithms have been proposed with this conjecture, and they parallel the two "quantum" algorithms put forward by molecular connectivity for atoms with n > 2. Nine properties of five classes of compounds have been tested: the molecular polarizabilities of a class of organic compounds, the dipole moment, molar refraction, boiling points, ionization energies, and parachor of a series of halomethanes, the lattice enthalpy of metal halides, the rates of hydrogen abstraction of chlorofluorocarbons, and the pED(50) of phenylalkylamines. The two tested algorithms based on the odd complete graph conjecture give rise to a highly interesting model of the nine properties, and three of them can even be modeled by the same set of basis indices. Interesting is the role of some basis indices all along the model.
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Affiliation(s)
- Lionello Pogliani
- Dipartimento di Chimica, Università della Calabria, 87030 Rende (CS), Italy.
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Galvez J. Prediction of molecular volume and surface of alkanes by molecular topology. JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES 2003; 43:1231-9. [PMID: 12870916 DOI: 10.1021/ci034036x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular volume and molecular surface are expressed as a function of topological degree in alkane graphs. This allows not only a straightforward approach to calculate such physicochemical magnitudes but also an interpretation of the role of the local vertex invariant (LOVI) or valence degree, delta, as well as the connectivity indices in the prediction of physicochemical properties. The interpretation is based on the concept of molecular accessibility (as introduced by Estrada, J. Phys. Chem. A 2002, 106, 9085) for which precise mathematical definitions are provided.
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Affiliation(s)
- Jorge Galvez
- Molecular Connectivity & Drug Design Research Unit, Department of Physical Chemistry, Faculty of Pharmacy, University of Valencia, Av. V.A. Estelles s.n., 46100-Burjasot, Valencia, Spain.
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Abstract
The development of molecular connectivity concept and some of its key elements - Randić's inverse-square-root function and the detailed subgraph characterization - are analyzed. The concept of overall connectivity recently advanced is presented as a next step in unfolding the ideas of molecular connectivity by combining them with those of molecular complexity. Definitions of overall connectivity index, eth-order overall connectivities, and overall connectivity vector are presented along with formulae for calculating these sets of topological indices for several classes of graphs of chemical relevance. Based on sums of adjacencies over all subgraphs (or up to a limiting subgraph size in large molecules), the overall connectivities increase both with molecule size and complexity, as expressed in branching and cyclicity of molecular skeleton. When applied to molecules containing heteroatoms, valence overall connectivities are constructed employing the Kier and Hall scheme. The usefulness of the novel indices is demonstrated by modeling physicochemical properties of alkane compounds. A detailed comparison is made with other models derived for the same set of compounds, proceeding from molecular connectivity, as well as with two other probe connectivity functions--the overall connectivity versions of the second Zagreb index, and a derivative inverse function of this index. The favorable comparisons indicate the need of molecular connectivity paradigm revisiting, and show the potential of the overall connectivity indices for QSPR/QSAR applications.
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Affiliation(s)
- D Bonchev
- Department of Marine Sciences, Texas A&M University, Galveston 77551, USA.
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Abstract
The simple molecular connectivity indices are interpreted as summations of bond accessibilities to bimolecular encounters with another, identical molecule. To transcend this model, a molecule is treated as disjecta membra with each bond modeled as a discrete cell in a dynamic simulation of many molecules. Each bond accessibility is transformed into a cellular automata rule. The dynamics are run for each of 38 alkanes, recording the average number of cell encounters, beta. The beta values show a high correlation with the boiling points. The significance of the bond accessibilities and the concept of intermolecular encounters explaining the molecular connectivity indices is supported by these findings.
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Affiliation(s)
- L B Kier
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond 23298-0540, USA.
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Kiralj R, Ferreira MMC. Predicting bond lengths in planar benzenoid polycyclic aromatic hydrocarbons: a chemometric approach. JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES 2002; 42:508-23. [PMID: 12086508 DOI: 10.1021/ci010063g] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Two hundred and twenty-three aromatic carbon-carbon bond lengths in high precision crystal structures containing 22 planar condensed benzenoid polycyclic aromatic hydrocarbons (PB-PAHs) were related to the Pauling pi-bond order, its analogue corrected to crystal packing effects, the number of hexagonal rings around the bond, and the numbers of carbons atoms around the bond at topological distance one and two. Principal Component Analysis (PCA) showed that the bond lengths in PB-PAHs are at least two-dimensional phenomenon, with well pronounced classification into 12 types of bonds, as confirmed with Hierachical Cluster Analysis (HCA). Consequently, Multiple Linear Regression (MLR) and Partial Least Squares (PLS) models were superior to univariate models, reducing the degeneration of the data set and improving the estimation of Julg's structural aromaticity index. The approximate regression models based on topological descriptors only were built for fast and easy prediction of bond lengths and bond orders in PB-PAHs.
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Affiliation(s)
- R Kiralj
- Laboratório de Quimiometria Teórica e Aplicada, Instituto de Química, Universidade Estadual de Campinas, Campinas, SP, 13083-970, Brazil.
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Pogliani L. Topics in molecular modeling: dual indices, quality of modeling and missing information, truncation. ACTA ACUST UNITED AC 2002. [DOI: 10.1016/s0166-1280(01)00746-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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García-Domenech R, de Julián-Ortiz JV. Prediction of Indices of Refraction and Glass Transition Temperatures of Linear Polymers by Using Graph Theoretical Indices. J Phys Chem B 2002. [DOI: 10.1021/jp012360u] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- R. García-Domenech
- Unidad de Investigación de Diseño de Fármacos y Conectividad Molecular, Departamento de Química Física, Facultat de Farmàcia, Universitat de València, Spain
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Estrada E, Molina E. 3D connectivity indices in QSPR/QSAR studies. JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES 2001; 41:791-7. [PMID: 11410059 DOI: 10.1021/ci000156i] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Topographic (3D) molecular connectivity indices based on molecular graphs weighted with quantum chemical parameters are used in QSPR and QSAR studies. These descriptors were compared to 2D connectivity indices (vertex and edge ones) and to quantum chemical descriptors in modeling partition coefficient (log P) and antibacterial activity of 2-furylethylene derivatives. In describing log P the 3D connectivity indices produced a significant improvement (more than 29%) in the predictive capacity of the model compared to those derived with topological and quantum chemical descriptors. The best linear discriminant model for classifying antibacterial activity of these compounds was also obtained with the use of 3D connectivity indices. The global percent of good classification obtained with 3D and 2D connectivity as well as quantum chemical descriptors were 94.1, 91.2, and 88.2, respectively. In general, all these models predict correctly the antibacterial activity of a set of nine new 2-furylethylene derivatives. The best result is obtained with 3D connectivity indices that classified correctly 100% of these compounds versus 88.9% obtained with 2D connectivity or quantum chemical descriptors.
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Affiliation(s)
- E Estrada
- Faculty of Pharmacy, Department of Organic Chemistry, University of Santiago de Compostela, Santiago de Compostela 15706, Spain.
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Mishra RK, Garcia-Domenech R, Galvez J. Getting discriminant functions of antibacterial activity from physicochemical and topological parameters. JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES 2001; 41:387-93. [PMID: 11277727 DOI: 10.1021/ci000303c] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Linear discriminant analysis has been demonstrated to be a very useful tool in the selection and design of new drugs. Up to now we have used it through the search of a topological pattern of activity. In this work our goal is to calculate a complete set of physicochemical parameters using semiempirical (quantum chemical) calculations as well as topological indices (TIs) and try to find out any discriminant function for antibacterial activity through the combined use of both types of descriptors. The physicochemical parameters, such as heat of formation, HOMO, LUMO, dipole moment, polarizability, hyperpolarizability, PM3 generated IR vibrational frequencies, etc., were calculated using PM3 Hamiltonian implemented within the MOPAC97 package. Among the TIs, connectivity as well as topological charge indices stands as the most representatives. The obtained results suggest that one of the maxima and minima vibrational frequencies play an important role in the antibacterial activity. These frequencies are associated with the torsional molecular vibration (N3) and the stretching vibration (N5) of X-H groups (X = C, N, O). Furthermore, the differences between the maxima and minima values showed an even better discriminant ability than the values themselves. The additional use of the topological indices provided a clear improvement in the discriminant function and also provided a straightforward way to predict the values of such frequencies, so that the results can be applied to a large set of compounds searching for new candidates as antibacterials.
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Affiliation(s)
- R K Mishra
- Drug Design & Molecular Connectivity Research Unit, Department of Physical Chemistry, Faculty of Pharmacy, University of Valencia, Avenida V.A. Estellés s.n. 46100-Burjasot, Valencia, Spain
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Pogliani L. From molecular connectivity indices to semiempirical connectivity terms: recent trends in graph theoretical descriptors. Chem Rev 2000; 100:3827-58. [PMID: 11749329 DOI: 10.1021/cr0004456] [Citation(s) in RCA: 140] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- L Pogliani
- Dipartimento di Chimica, Università della Calabria, 87030 Rende, Italy
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Tretiak S, Zhang WM, Chernyak V, Mukamel S. Excitonic couplings and electronic coherence in bridged naphthalene dimers. Proc Natl Acad Sci U S A 1999; 96:13003-8. [PMID: 10557262 PMCID: PMC23889 DOI: 10.1073/pnas.96.23.13003] [Citation(s) in RCA: 92] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The electronic excitations of naphthalene and a family of bridged naphthalene dimers are calculated and analyzed by using the Collective Electronic Oscillator method combined with the oblique Lanczos algorithm. All experimentally observed trends in absorption profiles and radiative lifetimes are reproduced. Each electronic excitation is linked to the corresponding real-space transition density matrix, which represents the motions of electrons and holes created in the molecule by photon absorption. Two-dimensional plots of these matrices help visualize the degree of exciton localization and explain the dependence of the electronic interaction between chromophores on their separation.
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Affiliation(s)
- S Tretiak
- Department of Chemistry and Rochester Theory Center for Optical Science and Engineering, University of Rochester, P.O. Box 270216, Rochester, NY 14627-0216, USA
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Estrada E. Connectivity polynomial and long-range contributions in the molecular connectivity model. Chem Phys Lett 1999. [DOI: 10.1016/s0009-2614(99)01007-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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