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Oña OB, De Clercq O, Alcoba DR, Torre A, Lain L, Van Neck D, Bultinck P. Atom and Bond Fukui Functions and Matrices: A Hirshfeld-I Atoms-in-Molecule Approach. Chemphyschem 2016; 17:2881-9. [PMID: 27381271 DOI: 10.1002/cphc.201600433] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Indexed: 11/09/2022]
Abstract
The Fukui function is often used in its atom-condensed form by isolating it from the molecular Fukui function using a chosen weight function for the atom in the molecule. Recently, Fukui functions and matrices for both atoms and bonds separately were introduced for semiempirical and ab initio levels of theory using Hückel and Mulliken atoms-in-molecule models. In this work, a double partitioning method of the Fukui matrix is proposed within the Hirshfeld-I atoms-in-molecule framework. Diagonalizing the resulting atomic and bond matrices gives eigenvalues and eigenvectors (Fukui orbitals) describing the reactivity of atoms and bonds. The Fukui function is the diagonal element of the Fukui matrix and may be resolved in atom and bond contributions. The extra information contained in the atom and bond resolution of the Fukui matrices and functions is highlighted. The effect of the choice of weight function arising from the Hirshfeld-I approach to obtain atom- and bond-condensed Fukui functions is studied. A comparison of the results with those generated by using the Mulliken atoms-in-molecule approach shows low correlation between the two partitioning schemes.
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Affiliation(s)
- Ofelia B Oña
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas, Universidad Nacional de la Plata, CCT La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, Diag. 113 y 64 (s/n), Sucursal 4, CC 16, 1900, La Plata, Argentina
| | - Olivier De Clercq
- Department of Inorganic and Physical Chemistry, Ghent University, Krijgslaan 281 (S3), 9000, Gent, Belgium
| | - Diego R Alcoba
- Departamento de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, 1428 Buenos Aires (Argentina), Instituto de Física de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Universitaria, 1428 Buenos, Aires, Argentina
| | - Alicia Torre
- Departamento de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco, Apdo. 644, E-48080, Bilbao, Spain
| | - Luis Lain
- Departamento de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco, Apdo. 644, E-48080, Bilbao, Spain
| | - Dimitri Van Neck
- Center for Molecular Modeling, Ghent University, Technologiepark 903, B-9052, Zwijnaarde, Belgium
| | - Patrick Bultinck
- Department of Inorganic and Physical Chemistry, Ghent University, Krijgslaan 281 (S3), 9000, Gent, Belgium.
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Morales-Bayuelo A. Analyzing the substitution effect on the CoMFA results within the framework of density functional theory (DFT). J Mol Model 2016; 22:164. [PMID: 27329189 DOI: 10.1007/s00894-016-3036-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 06/09/2016] [Indexed: 10/21/2022]
Abstract
Though QSAR was originally developed in the context of physical organic chemistry, it has been applied very extensively to chemicals (drugs) which act on biological systems, in this idea one of the most important QSAR methods is the 3D QSAR model. However, due to the complexity of understanding the results it is necessary to postulate new methodologies to highlight their physical-chemical meaning. In this sense, this work postulates new insights to understand the CoMFA results using molecular quantum similarity and chemical reactivity descriptors within the framework of density functional theory. To obtain these insights a simple theoretical scheme involving quantum similarity (overlap, coulomb operators, their euclidean distances) and chemical reactivity descriptors such as chemical potential (μ), hardness (ɳ), softness (S), electrophilicity (ω), and the Fukui functions, was used to understand the substitution effect. In this sense, this methodology can be applied to analyze the biological activity and the stabilization process in the non-covalent interactions on a particular molecular set taking a reference compound.
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Affiliation(s)
- Alejandro Morales-Bayuelo
- Grupo de Química Cuántica y Teórica de la Universidad de Cartagena, Facultad de Ciencias, Programa de Química, Cartagena de Indias, Colombia. .,FONDECYT Postdoctoral Project N0 3150035, Universidad de Talca, Talca, Chile.
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Ginex T, Muñoz-Muriedas J, Herrero E, Gibert E, Cozzini P, Luque FJ. Development and validation of hydrophobic molecular fields derived from the quantum mechanical IEF/PCM-MST solvation models in 3D-QSAR. J Comput Chem 2016; 37:1147-62. [DOI: 10.1002/jcc.24305] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 12/17/2015] [Accepted: 12/17/2015] [Indexed: 12/15/2022]
Affiliation(s)
- Tiziana Ginex
- Dipartimento Di Scienze Degli Alimenti; University of Parma; Parco Area Delle Scienze 59/a Parma 43121 Italy
| | - Jordi Muñoz-Muriedas
- GlaxoSmithKline; Medicines Research Centre; Gunnels Wood Road Stevenage SG1 2NY United Kingdom
| | - Enric Herrero
- Pharmacelera, Jordi Girona 1-3, Campus Nord Universitat Politècnica De Catalunya; Edifici K2M Barcelona 08034 Spain
| | - Enric Gibert
- Pharmacelera, Jordi Girona 1-3, Campus Nord Universitat Politècnica De Catalunya; Edifici K2M Barcelona 08034 Spain
| | - Pietro Cozzini
- Dipartimento Di Scienze Degli Alimenti; University of Parma; Parco Area Delle Scienze 59/a Parma 43121 Italy
| | - F. J. Luque
- Department of Chemical Physics and Institut De Biomedicina (IBUB), Faculty of Pharmacy; University of Barcelona; Av. Prat De La Riba 171 Santa Coloma De Gramenet 08921 Spain
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4
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Bultinck P, Cardenas C, Fuentealba P, Johnson PA, Ayers PW. How to Compute the Fukui Matrix and Function for Systems with (Quasi-)Degenerate States. J Chem Theory Comput 2013; 10:202-10. [DOI: 10.1021/ct400874d] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Patrick Bultinck
- Ghent University, Department of Inorganic and Physical Chemistry, Krijgslaan 281 (S3), 9000 Gent, Belgium
| | - Carlos Cardenas
- Departamento
de Física, Facultad de Ciencias, Universidad de Chile, Casilla 653, Santiago, Chile and Centro para el desarrollo de la
Nanociencias y Nanotecnologia, CEDENNA,
Av. Ecuador 3493, Santiago, Chile
| | - Patricio Fuentealba
- Departamento
de Física, Facultad de Ciencias, Universidad de Chile, Casilla 653, Santiago, Chile and Centro para el desarrollo de la
Nanociencias y Nanotecnologia, CEDENNA,
Av. Ecuador 3493, Santiago, Chile
| | - Paul A. Johnson
- Dept. of Chemistry and Chemical Biology, McMaster University, Hamilton ON Canada L8S 4M1
| | - Paul W. Ayers
- Dept. of Chemistry and Chemical Biology, McMaster University, Hamilton ON Canada L8S 4M1
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El Kerdawy A, Güssregen S, Matter H, Hennemann M, Clark T. Quantum Mechanics-Based Properties for 3D-QSAR. J Chem Inf Model 2013; 53:1486-502. [DOI: 10.1021/ci400181b] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Ahmed El Kerdawy
- Computer-Chemie-Centrum, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nägelsbachstraβe
25, 91052 Erlangen, Germany
| | - Stefan Güssregen
- Sanofi-Aventis Deutschland GmbH, R&D, LGCR, Structure, Design and Informatics, 65926 Frankfurt am Main, Germany
| | - Hans Matter
- Sanofi-Aventis Deutschland GmbH, R&D, LGCR, Structure, Design and Informatics, 65926 Frankfurt am Main, Germany
| | - Matthias Hennemann
- Computer-Chemie-Centrum, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nägelsbachstraβe
25, 91052 Erlangen, Germany
- Interdisciplinary Center for Molecular
Materials, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nägelsbachstraβe 49, 91052 Erlangen, Germany
| | - Timothy Clark
- Computer-Chemie-Centrum, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nägelsbachstraβe
25, 91052 Erlangen, Germany
- Interdisciplinary Center for Molecular
Materials, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nägelsbachstraβe 49, 91052 Erlangen, Germany
- Centre for Molecular Design, University of Portsmouth, King Henry Building, Portsmouth
PO1 2DY, United Kingdom
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Chadha N, Tiwari AK, Kumar V, Milton MD, Mishra AK. Perception into hypoxia selectivity and electronic features of symmetrically substituted bisthiosemicarbazone ligands and their copper complexes: DFT and QM/MM docking. MEDCHEMCOMM 2013. [DOI: 10.1039/c2md20333b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Sridhar J, Liu J, Foroozesh M, Klein Stevens CL. Insights on cytochrome p450 enzymes and inhibitors obtained through QSAR studies. Molecules 2012; 17:9283-305. [PMID: 22864238 PMCID: PMC3666846 DOI: 10.3390/molecules17089283] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Revised: 07/24/2012] [Accepted: 07/26/2012] [Indexed: 11/28/2022] Open
Abstract
The cytochrome P450 (CYP) superfamily of heme enzymes play an important role in the metabolism of a large number of endogenous and exogenous compounds, including most of the drugs currently on the market. Inhibitors of CYP enzymes have important roles in the treatment of several disease conditions such as numerous cancers and fungal infections in addition to their critical role in drug-drug interactions. Structure activity relationships (SAR), and three-dimensional quantitative structure activity relationships (3D-QSAR) represent important tools in understanding the interactions of the inhibitors with the active sites of the CYP enzymes. A comprehensive account of the QSAR studies on the major human CYPs 1A1, 1A2, 1B1, 2A6, 2B6, 2C9, 2C19, 2D6, 2E1, 3A4 and a few other CYPs are detailed in this review which will provide us with an insight into the individual/common characteristics of the active sites of these enzymes and the enzyme-inhibitor interactions.
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Affiliation(s)
- Jayalakshmi Sridhar
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Dr., New Orleans, LA 70125, USA
| | - Jiawang Liu
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Dr., New Orleans, LA 70125, USA
| | - Maryam Foroozesh
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Dr., New Orleans, LA 70125, USA
- Author to whom correspondence should be addressed; ; Tel.: +1-504-520-5078; Fax: +1-504-520-7942
| | - Cheryl L. Klein Stevens
- Ogden College of Science & Engineering, Western Kentucky University, 1906 College Heights Blvd., Bowling Green, KY 42101, USA
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Rahnasto MK, Raunio HA, Wittekindt C, Salminen KA, Leppänen J, Juvonen RO, Poso A, Lahtela-Kakkonen MK. Identification of novel CYP2A6 inhibitors by virtual screening. Bioorg Med Chem 2011; 19:7186-93. [PMID: 22019468 DOI: 10.1016/j.bmc.2011.09.054] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Revised: 09/01/2011] [Accepted: 09/28/2011] [Indexed: 11/19/2022]
Abstract
The human CYP2A6 enzyme metabolises several xenobiotics including nicotine, the addictive component in tobacco. Reduced activity of CYP2A6, either for genetic reasons or by administering inhibitors of CYP2A6, reduces tobacco smoking. The aim was to design novel inhibitors of CYP2A6 using 3D-QSAR analysis combined with virtual screening. A 3D-QSAR model was utilised to identify the most important features of the inhibitors, and this knowledge was used to design inhibitors for CYP2A6. Chemical database screening yielded several potent inhibitor candidates such as alkylamine derivatives (compound no. 5, IC(50)=0.1 μM) and 1-benzothiophene-3-carbaldehyde that can be used as lead compounds in the development of drugs for smoking reduction therapy.
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Affiliation(s)
- Minna K Rahnasto
- School of Pharmacy, University of Eastern Finland, POB 1627, 70211 Kuopio, Finland.
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9
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Docking, molecular dynamics simulation studies, and structure-based QSAR model on cytochrome P450 2A6 inhibitors. Struct Chem 2011. [DOI: 10.1007/s11224-011-9874-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Mishra NK. Computational modeling of P450s for toxicity prediction. Expert Opin Drug Metab Toxicol 2011; 7:1211-31. [DOI: 10.1517/17425255.2011.611501] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Ma Y, Wang JG, Wang B, Li ZM. Integrating molecular docking, DFT and CoMFA/CoMSIA approaches for a series of naphthoquinone fused cyclic α-aminophosphonates that act as novel topoisomerase II inhibitors. J Mol Model 2010; 17:1899-909. [PMID: 21107989 DOI: 10.1007/s00894-010-0898-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2010] [Accepted: 11/08/2010] [Indexed: 11/29/2022]
Abstract
Since they are potential topoisomerase II (Topo II) inhibitors, naphthoquinone fused cyclic α-aminophosphonates display anticancer activity. In order to explore the inhibitory mechanisms of these compounds, they were docked into the active site of Topo II structure, which allowed their probable binding modes to be predicted. Some meaningful results concerning their structure-activity relationships were obtained from density functional theory calculations. Models based on quantitative comparative molecular field analysis and comparative molecular similarity index analysis were derived for the steric, electrostatic, hydrophobic and H-bonding features of the compounds. The present study provides valuable results that enhance our understanding of the anticancer activities of these inhibitors and will aid the rational drug design of novel Topo II inhibitors in the future.
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Affiliation(s)
- Yi Ma
- State-key Laboratory and Institute of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, China
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12
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Hasegawa K, Koyama M, Funatsu K. Quantitative Prediction of Regioselectivity Toward Cytochrome P450/3A4 Using Machine Learning Approaches. Mol Inform 2010; 29:243-9. [PMID: 27462767 DOI: 10.1002/minf.200900086] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2009] [Accepted: 02/11/2010] [Indexed: 11/11/2022]
Abstract
In the drug discovery process, it is important to know the properties of both drug candidates and their metabolites. Fast and precise prediction of metabolites is essential. However, it has been difficult to predict metabolites because of the complexity of the mechanism of cytochrome P450/3A4 (CYP 3A4), which is the main metabolite enzyme of drugs. In this study, we focus on the regioselectivity of CYP 3A4, i.e., the selectivity of metabolic sites. We have developed a model to predict the regioselectivity of drug candidates by using machine learning (ML) approaches.
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Affiliation(s)
- Kiyoshi Hasegawa
- Chugai Pharmaceutical Company, Kamakura Research, Laboratories, Kajiwara 200, Kamakura, Kanagawa 247-8530, Japan
| | - Michio Koyama
- Department of Chemical System Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan phone: (+81) 03-5841-7751 fax: (+81) 03-5841-7771
| | - Kimito Funatsu
- Department of Chemical System Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan phone: (+81) 03-5841-7751 fax: (+81) 03-5841-7771.
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13
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Van Damme S, Bultinck P. 3D QSAR based on conceptual DFT molecular fields: Antituberculotic activity. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.theochem.2009.10.031] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Abstract
Cytochrome P450 (CYP450) enzymes are predominantly involved in the Phase I metabolism of xenobiotics. Metabolic inhibition and induction can give rise to clinically important drug-drug interactions. Metabolic stability is a prerequisite for sustaining the therapeutically relevant concentrations, and very often drug candidates are sacrificed due to poor metabolic profiles. Computational tools such as quantitative structure-activity relationships are widely used to study different metabolic end points successfully to accelerate the drug discovery process. There are a lot of computational studies on clinically important CYPs already reported in recent years. But other clinically significant families are to yet be explored computationally. Powerfulness of quantitative structure-activity relationship will drive computational chemists to develop new potent and selective inhibitors of different classes of CYPs for the treatment of different diseases with least drug-drug interactions. Furthermore, there is a need to enhance the accuracy, interpretability and confidence in the computational models in accelerating the drug discovery pathways.
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Affiliation(s)
- Kunal Roy
- Jadavpur University, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Drug Theoretics and Cheminformatics Lab, Kolkata 700 032, India.
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