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Messina PV, Besada-Porto JM, González-Díaz H, Ruso JM. Self-Assembled Binary Nanoscale Systems: Multioutput Model with LFER-Covariance Perturbation Theory and an Experimental-Computational Study of NaGDC-DDAB Micelles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:12009-12018. [PMID: 26484726 DOI: 10.1021/acs.langmuir.5b03074] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Studies of the self-aggregation of binary systems are of both theoretical and practical importance. They provide an opportunity to investigate the influence of the molecular structure of the hydrophobe on the nonideality of mixing. On the other hand, linear free energy relationship (LFER) models, such as Hansch's equations, may be used to predict the properties of chemical compounds such as drugs or surfactants. However, the task becomes more difficult once we want to predict simultaneaously the effect over multiple output properties of binary systems of perturbations under multiple input experimental boundary conditions (b(j)). As a consequence, we need computational chemistry or chemoinformatics models that may help us to predict different properties of the autoaggregation process of mixed surfactants under multiple conditions. In this work, we have developed the first model that combines perturbation theory (PT) and LFER ideas. The model uses as input covariance PT operators (CPTOs). CPTOs are calculated as the difference between covariance ΔCov((i)μ(k)) functions before and after multiple perturbations in the binary system. In turn, covariances calculated as the product of two Box-Jenkins operators (BJO) operators. BJOs are used to measure the deviation of the structure of different chemical compounds from a set of molecules measured under a given subset of experimental conditions. The best CPT-LFER model found predicted the effects of 25,000 perturbations over 9 different properties of binary systems. We also reported experimental studies of different experimental properties of the binary system formed by sodium glycodeoxycholate and didodecyldimethylammonium bromide (NaGDC-DDAB). Last, we used our CPT-LFER model to carry out a 1000 data point simulation of the properties of the NaGDC-DDAB system under different conditions not studied experimentally.
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Affiliation(s)
- Paula V Messina
- Department of Chemistry, INQUISUR-CONICET, Universidad Nacional del Sur , 8000 Bahía Blanca, Argentina
| | - Jose Miguel Besada-Porto
- Soft Matter and Molecular Biophysics Group, Department of Applied Physics, University of Santiago de Compostela , Santiago de Compostela E-15782, Spain
| | - Humberto González-Díaz
- Department of Organic Chemistry II, Faculty of Science and Technology, University of the Basque Country UPV/EHU , 48940 Leioa, Spain
- IKERBASQUE, Basque Foundation for Science, 48011 Bilbao, Spain
| | - Juan M Ruso
- Soft Matter and Molecular Biophysics Group, Department of Applied Physics, University of Santiago de Compostela , Santiago de Compostela E-15782, Spain
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Margraf JT, Hennemann M, Meyer B, Clark T. EMPIRE: a highly parallel semiempirical molecular orbital program: 2: periodic boundary conditions. J Mol Model 2015; 21:144. [PMID: 25983105 PMCID: PMC4435633 DOI: 10.1007/s00894-015-2692-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2015] [Accepted: 04/27/2015] [Indexed: 11/20/2022]
Abstract
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Affiliation(s)
- Johannes T Margraf
- Computer-Chemie-Centrum and Interdisciplinary Center for Molecular Materials, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nägelsbachstraße 25, 91052, Erlangen, Germany
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Liu Y, Buendía-Rodríguez G, Peñuelas-Rívas CG, Tan Z, Rívas-Guevara M, Tenorio-Borroto E, Munteanu CR, Pazos A, González-Díaz H. Experimental and computational studies of fatty acid distribution networks. MOLECULAR BIOSYSTEMS 2015; 11:2964-77. [DOI: 10.1039/c5mb00325c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
A new PT-LFER model is useful for predicting a distribution network in terms of specific fatty acid distribution.
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Affiliation(s)
- Yong Liu
- Faculty of Veterinary Medicine and Animal Science
- Autonomous University of the State of Mexico
- Toluca
- Mexico
- Key Laboratory of Subtropical Agro-ecological Engineering
| | - Germán Buendía-Rodríguez
- National Center for Disciplinary Research on Animal Physiology and Breeding
- National Institute of Forestry
- Agriculture and Livestock Research
- Queretaro
- Mexico
| | | | - Zhiliang Tan
- Key Laboratory of Subtropical Agro-ecological Engineering
- Institute of Subtropical Agriculture, the Chinese Academy of Sciences
- Changsha
- P. R. China
| | - María Rívas-Guevara
- Ethnobiology and Biodiversity Research Center
- Chapingo Autonomous University
- Texcoco
- Mexico
| | - Esvieta Tenorio-Borroto
- Faculty of Veterinary Medicine and Animal Science
- Autonomous University of the State of Mexico
- Toluca
- Mexico
| | | | | | - Humberto González-Díaz
- Department of Organic Chemistry II
- Faculty of Science and Technology
- University of the Basque Country UPV/EHU
- Leioa
- Spain
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Beck B, Geppert T. Industrial applications of in silico ADMET. J Mol Model 2014; 20:2322. [PMID: 24972798 DOI: 10.1007/s00894-014-2322-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 05/27/2014] [Indexed: 11/26/2022]
Abstract
Quantitative structure activity relationship (QSAR) modeling has been in use for several decades now. One branch of it, in silico ADMET, became more and more important since the late 1990s as studies indicated that poor pharmacokinetics and toxicity were important causes of costly late-stage failures in drug development. In this paper we describe some of the available methods and best practice for the different stages of the in silico model building process. We also describe some more recent developments, like automated model building and the prediction probability. Finally we will discuss the use of in silico ADMET for "big data" and the importance and possible further development of interpretable models.
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Affiliation(s)
- Bernd Beck
- Department of Lead Identification and Optimization Support, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorferstrasse 65, 88397, Biberach an der Riss, Germany,
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Dral PO. The unrestricted local properties: application in nanoelectronics and for predicting radicals reactivity. J Mol Model 2014; 20:2134. [PMID: 24535109 DOI: 10.1007/s00894-014-2134-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Accepted: 12/27/2013] [Indexed: 12/12/2022]
Abstract
The local electron affinity (EA(L)) and the local ionization energy (IE(L)) are successfully used for predicting properties of closed-shell species for drug design and for nanoelectronics. Here the respective unrestricted Hartree-Fock variants of EA(L) and IE(L), i.e., the unrestricted local electron affinity (UHF-EA(L)) and ionization energy (UHF-IE(L)), have been shown to be useful for predicting properties of open-shell species. UHF-EA(L) and UHF-IE(L) have been applied for explaining unique electronic properties of an exemplary nanomaterial carbon peapod. It is also demonstrated that UHF-EA(L) is useful for predicting and better understanding reactivity of radicals related to alkanes activation.
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Affiliation(s)
- Pavlo O Dral
- Computer-Chemie-Centrum and Interdisciplinary Center for Molecular Materials, University of Erlangen-Nuremberg, Nägelsbachstr. 25, 91052, Erlangen, Germany,
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6
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Ma L, Zhao DX, Yang ZZ. A software tool for visualization of molecular face (VMF) by improving marching cubes algorithm. COMPUT THEOR CHEM 2014. [DOI: 10.1016/j.comptc.2013.11.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Development of in silico filters to predict activation of the pregnane X receptor (PXR) by structurally diverse drug-like molecules. Bioorg Med Chem 2012; 20:5352-65. [PMID: 22560839 DOI: 10.1016/j.bmc.2012.04.020] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Revised: 03/28/2012] [Accepted: 04/07/2012] [Indexed: 01/22/2023]
Abstract
The pregnane X receptor (PXR), a member of the nuclear hormone superfamily, regulates the expression of several enzymes and transporters involved in metabolically relevant processes. The significant induction of CYP450 enzymes by PXR, in particular CYP3A4, might significantly alter the metabolism of prescribed drugs. In order to early identify molecules in drug discovery with a potential to activate PXR as antitarget, we developed fast and reliable in silico filters by ligand-based QSAR techniques. Two classification models were established on a diverse dataset of 434 drug-like molecules. A second augmented set allowed focusing on interesting regions in chemical space. These classifiers are based on decision trees combined with a genetic algorithm based variable selection to arrive at predictive models. The classifier for the first dataset on 29 descriptors showed good performance on a test set with a correct classification of both 100% for PXR activators and non-activators plus 87% for activators and 83% for non-activators in an external dataset. The second classifier then correctly predicts 97% activators and 91% non-activators in a test set and 94% for activators and 64% non-activators in an external set of 50 molecules, which still qualifies for application as a filter focusing on PXR activators. Finally a quantitative model for PXR activation for a subset of these molecules was derived using a regression-tree approach combined with GA variable selection. This final model shows a predictive r(2) of 0.774 for the test set and 0.452 for an external set of 33 molecules. Thus, the combination of these filters consistently provide guidelines for lowering PXR activation in novel candidate molecules.
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Muehlbacher M, Kerdawy AE, Kramer C, Hudson B, Clark T. Conformation-Dependent QSPR Models: logPOW. J Chem Inf Model 2011; 51:2408-16. [DOI: 10.1021/ci200276v] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Markus Muehlbacher
- Computer-Chemie-Centrum, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nägelsbachstrasse 25, 91052 Erlangen, Germany
- Psychiatrische und Psychotherapeutische Klinik, Friedrich-Alexander-Universität Erlangen-Nürnberg, Schwabachanlage 6, 91054 Erlangen, Germany
| | - Ahmed El Kerdawy
- Computer-Chemie-Centrum, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nägelsbachstrasse 25, 91052 Erlangen, Germany
| | - Christian Kramer
- Novartis Pharma AG, Forum 1, Novartis Campus, CH-4056 Basel, Switzerland
| | - Brian Hudson
- Centre for Molecular Design, University of Portsmouth, Mercantile House, Portsmouth PO1 2EG, United Kingdom
| | - Timothy Clark
- Computer-Chemie-Centrum, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nägelsbachstrasse 25, 91052 Erlangen, Germany
- Centre for Molecular Design, University of Portsmouth, Mercantile House, Portsmouth PO1 2EG, United Kingdom
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Affiliation(s)
- Christian Kramer
- Computer-Chemie-Centrum and Interdisciplinary Center for Molecular Materials, Friedrich-Alexander Universität Erlangen-Nürnberg, Nägelsbachstrasse 52, 91052 Erlangen (Germany); Department of Lead Discovery, Boehringer−Ingelheim Pharma GmbH & Co. KG, 88397 Biberach (Germany); and Centre for Molecular Design, University of Portsmouth, Mercantile House, Hampshire Terrace, Portsmouth, PO1 2EG, United Kingdom
| | - Bernd Beck
- Computer-Chemie-Centrum and Interdisciplinary Center for Molecular Materials, Friedrich-Alexander Universität Erlangen-Nürnberg, Nägelsbachstrasse 52, 91052 Erlangen (Germany); Department of Lead Discovery, Boehringer−Ingelheim Pharma GmbH & Co. KG, 88397 Biberach (Germany); and Centre for Molecular Design, University of Portsmouth, Mercantile House, Hampshire Terrace, Portsmouth, PO1 2EG, United Kingdom
| | - Timothy Clark
- Computer-Chemie-Centrum and Interdisciplinary Center for Molecular Materials, Friedrich-Alexander Universität Erlangen-Nürnberg, Nägelsbachstrasse 52, 91052 Erlangen (Germany); Department of Lead Discovery, Boehringer−Ingelheim Pharma GmbH & Co. KG, 88397 Biberach (Germany); and Centre for Molecular Design, University of Portsmouth, Mercantile House, Hampshire Terrace, Portsmouth, PO1 2EG, United Kingdom
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10
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Clark T. The local electron affinity for non-minimal basis sets. J Mol Model 2010; 16:1231-8. [DOI: 10.1007/s00894-009-0607-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2009] [Accepted: 09/30/2009] [Indexed: 12/12/2022]
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Livingstone DJ, Clark T, Ford MG, Hudson BD, Whitley DC. QSAR studies using the parashift system. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2008; 19:285-302. [PMID: 18484499 DOI: 10.1080/10629360802085041] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
A novel way of describing molecules in terms of their surfaces and local properties at the surfaces is described. The use of these surfaces and properties to explain chemical reactivity and model simple molecular properties has already been demonstrated. This study reports an examination of the use of these descriptions of molecules to model a simple chemical interaction (complex formation) and a diverse set of mutagens. Both of these systems have been modelled successfully and the results are discussed.
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de Groot MJ. Designing better drugs: predicting cytochrome P450 metabolism. Drug Discov Today 2006; 11:601-6. [PMID: 16793528 DOI: 10.1016/j.drudis.2006.05.001] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2006] [Revised: 04/21/2006] [Accepted: 05/10/2006] [Indexed: 10/24/2022]
Abstract
Many 3D ligand-based and structure-based computational approaches have been used to predict, and thus help explain, the metabolism catalyzed by the enzymes of the cytochrome P450 superfamily (P450s). P450s are responsible for >90% of the metabolism of all drugs, so the computational prediction of metabolism can help to design out drug-drug interactions in the early phases of the drug discovery process. Computational methodologies have focused on a few P450s that are directly involved in drug metabolism. The recently derived crystal structures for human P450s enable better 3D modelling of these important metabolizing enzymes. Models derived for P450s have evolved from simple comparisons of known substrates to more-elaborate experiments that require considerable computer power involving 3D overlaps and docking experiments. These models help to explain and, more importantly, predict the involvement of P450s in the metabolism of specific compounds and guide the drug-design process.
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Affiliation(s)
- Marcel J de Groot
- Sandwich Chemistry, Pfizer Global Research & Development, Sandwich Laboratories, Kent CT13 9NJ, UK.
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