51
|
|
52
|
Peón A, Coderch C, Gago F, González-Bello C. Comparative binding energy COMBINE analysis for understanding the binding determinants of type II dehydroquinase inhibitors. ChemMedChem 2013; 8:740-7. [PMID: 23450741 DOI: 10.1002/cmdc.201300013] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Indexed: 11/08/2022]
Abstract
Herein we report comparative binding energy (COMBINE) analyses to derive quantitative structure-activity relationship (QSAR) models that help rationalize the determinants of binding affinity for inhibitors of type II dehydroquinase (DHQ2), the third enzyme of the shikimic acid pathway. Independent COMBINE models were derived for Helicobacter pylori and Mycobacterium tuberculosis DHQ2, which is an essential enzyme in both these pathogenic bacteria that has no counterpart in human cells. These studies quantify the importance of the hydrogen bonding interactions between the ligands and the water molecule involved in the DHQ2 reaction mechanism. They also highlight important differences in the ligand interactions with the interface pocket close to the active site that could provide guides for future inhibitor design.
Collapse
Affiliation(s)
- Antonio Peón
- Centro Singular de Investigación en Química Biológica y Materiales, Moleculares CIQUS, Universidad de Santiago de Compostela calle Jenaro de la Fuente s/n, 15782 Santiago de Compostela Spain
| | | | | | | |
Collapse
|
53
|
Gertzen CGW, Gohlke H. From Hansch-Fujita Analysis to AFMoC: A Road to Structure-Based QSAR. Mol Inform 2012; 31:698-704. [PMID: 27476451 DOI: 10.1002/minf.201200015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Accepted: 07/10/2012] [Indexed: 11/05/2022]
Abstract
Since the pioneering effort of Hansch and Fujita, quantitative structure-activity relationships (QSAR) have proved valuable in optimizing lead structures. Enriching classical 3D-QSAR analysis, which exploits the three-dimensional structure of ligands, with structural information of the target has helped to improve the interpretability of the derived models and to increase their predictive power. One such method is the Adaption of Fields for Molecular Comparison (AFMoC) approach where protein-specifically adapted knowledge-based pair-potentials are tailored to one particular protein by considering additional structural and energetic information about ligands. Here, we summarize applications of AFMoC, describe recent developments, and provide an outlook on how to improve the method.
Collapse
Affiliation(s)
- Christoph G W Gertzen
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf fax: +49-211-8113847
| | - Holger Gohlke
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf fax: +49-211-8113847.
| |
Collapse
|
54
|
Fukunishi Y, Nakamura H. Statistical estimation of the protein-ligand binding free energy based on direct protein-ligand interaction obtained by molecular dynamics simulation. Pharmaceuticals (Basel) 2012; 5:1064-79. [PMID: 24281257 PMCID: PMC3816655 DOI: 10.3390/ph5101064] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Revised: 09/19/2012] [Accepted: 09/21/2012] [Indexed: 11/28/2022] Open
Abstract
We have developed a method for estimating protein-ligand binding free energy (DG) based on the direct protein-ligand interaction obtained by a molecular dynamics simulation. Using this method, we estimated the DG value statistically by the average values of the van der Waals and electrostatic interactions between each amino acid of the target protein and the ligand molecule. In addition, we introduced fluctuations in the accessible surface area (ASA) and dihedral angles of the protein-ligand complex system as the entropy terms of the DG estimation. The present method included the fluctuation term of structural change of the protein and the effective dielectric constant. We applied this method to 34 protein-ligand complex structures. As a result, the correlation coefficient between the experimental and calculated DG values was 0.81, and the average error of DG was 1.2 kcal/mol with the use of the fixed parameters. These results were obtained from a 2 nsec molecular dynamics simulation.
Collapse
Affiliation(s)
- Yoshifumi Fukunishi
- Biological Information Research Center (BIRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-3-26, Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Haruki Nakamura
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan;
| |
Collapse
|
55
|
Liu S, Fu R, Cheng X, Chen SP, Zhou LH. Exploring the binding of BACE-1 inhibitors using comparative binding energy analysis (COMBINE). BMC STRUCTURAL BIOLOGY 2012; 12:21. [PMID: 22925713 PMCID: PMC3533579 DOI: 10.1186/1472-6807-12-21] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2011] [Accepted: 08/03/2012] [Indexed: 01/14/2023]
Abstract
BACKGROUND The inhibition of the activity of β-secretase (BACE-1) is a potentially important approach for the treatment of Alzheimer disease. To explore the mechanism of inhibition, we describe the use of 46 X-ray crystallographic BACE-1/inhibitor complexes to derive quantitative structure-activity relationship (QSAR) models. The inhibitors were aligned by superimposing 46 X-ray crystallographic BACE-1/inhibitor complexes, and gCOMBINE software was used to perform COMparative BINding Energy (COMBINE) analysis on these 46 minimized BACE-1/inhibitor complexes. The major advantage of the COMBINE analysis is that it can quantitatively extract key residues involved in binding the ligand and identify the nature of the interactions between the ligand and receptor. RESULTS By considering the contributions of the protein residues to the electrostatic and van der Waals intermolecular interaction energies, two predictive and robust COMBINE models were developed: (i) the 3-PC distance-dependent dielectric constant model (built from a single X-ray crystal structure) with a q2 value of 0.74 and an SDEC value of 0.521; and (ii) the 5-PC sigmoidal electrostatic model (built from the actual complexes present in the Brookhaven Protein Data Bank) with a q2 value of 0.79 and an SDEC value of 0.41. CONCLUSIONS These QSAR models and the information describing the inhibition provide useful insights into the design of novel inhibitors via the optimization of the interactions between ligands and those key residues of BACE-1.
Collapse
Affiliation(s)
- Shu Liu
- Guangdong Province Key Laboratory of Functional Molecules in Oceanic Microorganism, Zhong Shan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, People’s Republic of China
- Department of Anatomy, Zhong Shan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, People’s Republic of China
| | - Rao Fu
- Department of Anatomy, Zhong Shan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, People’s Republic of China
| | - Xiao Cheng
- Department of Anatomy, Zhong Shan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, People’s Republic of China
| | - Sheng-Ping Chen
- Guangdong Province Key Laboratory of Functional Molecules in Oceanic Microorganism, Zhong Shan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, People’s Republic of China
| | - Li-Hua Zhou
- Department of Anatomy, Zhong Shan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, People’s Republic of China
| |
Collapse
|
56
|
Silvestri L, Ballante F, Mai A, Marshall GR, Ragno R. Histone Deacetylase Inhibitors: Structure-Based Modeling and Isoform-Selectivity Prediction. J Chem Inf Model 2012; 52:2215-35. [DOI: 10.1021/ci300160y] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Laura Silvestri
- Rome
Center for Molecular Design Dipartimento di Chimica e Tecnologie del
Farmaco, Facoltà di Farmacia e Medicina, ‡Istituto Pasteur—Fondazione
Cenci Bolognetti Dipartimento di Chimica e Tecnologie del Farmaco,
Facoltà di Farmacia e Medicina, Sapienza Università di Roma, P.le A. Moro 5, 00185 Rome,
Italy
| | - Flavio Ballante
- Rome
Center for Molecular Design Dipartimento di Chimica e Tecnologie del
Farmaco, Facoltà di Farmacia e Medicina, ‡Istituto Pasteur—Fondazione
Cenci Bolognetti Dipartimento di Chimica e Tecnologie del Farmaco,
Facoltà di Farmacia e Medicina, Sapienza Università di Roma, P.le A. Moro 5, 00185 Rome,
Italy
| | - Antonello Mai
- Rome
Center for Molecular Design Dipartimento di Chimica e Tecnologie del
Farmaco, Facoltà di Farmacia e Medicina, ‡Istituto Pasteur—Fondazione
Cenci Bolognetti Dipartimento di Chimica e Tecnologie del Farmaco,
Facoltà di Farmacia e Medicina, Sapienza Università di Roma, P.le A. Moro 5, 00185 Rome,
Italy
| | - Garland R. Marshall
- Rome
Center for Molecular Design Dipartimento di Chimica e Tecnologie del
Farmaco, Facoltà di Farmacia e Medicina, ‡Istituto Pasteur—Fondazione
Cenci Bolognetti Dipartimento di Chimica e Tecnologie del Farmaco,
Facoltà di Farmacia e Medicina, Sapienza Università di Roma, P.le A. Moro 5, 00185 Rome,
Italy
| | - Rino Ragno
- Rome
Center for Molecular Design Dipartimento di Chimica e Tecnologie del
Farmaco, Facoltà di Farmacia e Medicina, ‡Istituto Pasteur—Fondazione
Cenci Bolognetti Dipartimento di Chimica e Tecnologie del Farmaco,
Facoltà di Farmacia e Medicina, Sapienza Università di Roma, P.le A. Moro 5, 00185 Rome,
Italy
| |
Collapse
|
57
|
de Brito MA, Rodrigues CR, Cirino JJV, Araújo JQ, Honório T, Cabral LM, de Alencastro RB, Castro HC, Albuquerque MG. Residue-ligand interaction energy (ReLIE) on a receptor-dependent 3D-QSAR analysis of S- and NH-DABOs as non-nucleoside reverse transcriptase inhibitors. Molecules 2012; 17:7666-94. [PMID: 22732882 PMCID: PMC6269006 DOI: 10.3390/molecules17077666] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2012] [Revised: 06/02/2012] [Accepted: 06/05/2012] [Indexed: 11/16/2022] Open
Abstract
A series of 74 dihydroalkoxybenzyloxopyrimidines (DABOs), a class of highly potent non-nucleoside reverse transcriptase inhibitors (NNRTIs), was retrieved from the literature and studied by receptor-dependent (RD) three-dimensional quantitative structure-activity relationship (3D-QSAR) analysis to derive RD-3D-QSAR models. The descriptors in this new method are the steric and electrostatic interaction energies of the protein-ligand complexes (per residue) simulated by molecular dynamics, an approach named Residue-Ligand Interaction Energy (ReLIE). This study was performed using a training set of 59 compounds and the MKC-442/RT complex structure as reference. The ReLIE-3D-QSAR models were constructed and evaluated by genetic algorithm (GA) and partial least squares (PLS). In the best equations, at least one term is related to one of the amino acid residues of the p51 subunit: Asn136, Asn137, Glu138, and Thr139. This fact implies the importance of interchain interaction (p66-p51) in the equations that best describe the structure-activity relationship for this class of compounds. The best equation shows q² = 0.660, SE(cv) = 0.500, r² = 0.930, and SEE = 0.226. The external predictive ability of this best model was evaluated using a test set of 15 compounds. In order to design more potent DABO analogues as anti-HIV/AIDS agents, substituents capable of interactions with residues like Ile94, Lys101, Tyr181, and Tyr188 should be selected. Also, given the importance of the conserved Asn136, this residue could become an attractive target for the design of novel NNRTIs with improved potency and increased ability to avoid the development of drug-resistant viruses.
Collapse
Affiliation(s)
- Monique Araújo de Brito
- Laboratory of Computational Medicinal Chemistry (LabQMC), Faculty of Pharmacy, Fluminense Federal University (UFF), Niterói, RJ, 24241-000, Brazil
- Laboratory of Molecular Modeling (LabMMol), Program of Post-Graduation in Chemistry (PPGQu), Institute of Chemistry, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, 21941-909, Brazil
- Authors to whom correspondence should be addressed; (M.A.B.); (M.G.A.); Tel.: +55-21-2629-9599 (M.A.B.); +55-21-2562-7132 (M.G.A.)
| | - Carlos Rangel Rodrigues
- Laboratory of Molecular Modeling & QSAR (ModMolQSAR), Faculty of Pharmacy, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, 21941-590, Brazil
| | - José Jair Viana Cirino
- Laboratory of Molecular Modeling (LabMMol), Program of Post-Graduation in Chemistry (PPGQu), Institute of Chemistry, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, 21941-909, Brazil
| | - Jocley Queiroz Araújo
- Laboratory of Molecular Modeling (LabMMol), Program of Post-Graduation in Chemistry (PPGQu), Institute of Chemistry, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, 21941-909, Brazil
| | - Thiago Honório
- Laboratory of Molecular Modeling & QSAR (ModMolQSAR), Faculty of Pharmacy, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, 21941-590, Brazil
| | - Lúcio Mendes Cabral
- Laboratory of Molecular Modeling & QSAR (ModMolQSAR), Faculty of Pharmacy, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, 21941-590, Brazil
| | - Ricardo Bicca de Alencastro
- Laboratory of Molecular Modeling (LabMMol), Program of Post-Graduation in Chemistry (PPGQu), Institute of Chemistry, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, 21941-909, Brazil
| | - Helena Carla Castro
- Laboratory of Antibiotics, Biochemistry, Education and Molecular Modeling (LABiEMol), Institute of Biology, Fluminense Federal University (UFF), Niterói, RJ, 24210-130, Brazil
| | - Magaly Girão Albuquerque
- Laboratory of Molecular Modeling (LabMMol), Program of Post-Graduation in Chemistry (PPGQu), Institute of Chemistry, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, 21941-909, Brazil
- Authors to whom correspondence should be addressed; (M.A.B.); (M.G.A.); Tel.: +55-21-2629-9599 (M.A.B.); +55-21-2562-7132 (M.G.A.)
| |
Collapse
|
58
|
|
59
|
Rotili D, Samuele A, Tarantino D, Ragno R, Musmuca I, Ballante F, Botta G, Morera L, Pierini M, Cirilli R, Nawrozkij MB, Gonzalez E, Clotet B, Artico M, Esté JA, Maga G, Mai A. 2-(Alkyl/aryl)amino-6-benzylpyrimidin-4(3H)-ones as inhibitors of wild-type and mutant HIV-1: enantioselectivity studies. J Med Chem 2012; 55:3558-62. [PMID: 22428851 DOI: 10.1021/jm201308v] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The single enantiomers of two pyrimidine-based HIV-1 non-nucleoside reverse transcriptase inhibitors, 1 (MC1501) and 2 (MC2082), were tested in both cellular and enzyme assays. In general, the R forms were more potent than their S counterparts and racemates and (R)-2 was more efficient than (R)-1 and the reference compounds, with some exceptions. Interestingly, (R)-2 displayed a faster binding to K103N RT with respect to WT RT, while (R)-1 showed the opposite behavior.
Collapse
Affiliation(s)
- Dante Rotili
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma La Sapienza, P.le A. Moro 5, 00185 Rome, Italy
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
60
|
Kirchmair J, Williamson MJ, Tyzack JD, Tan L, Bond PJ, Bender A, Glen RC. Computational prediction of metabolism: sites, products, SAR, P450 enzyme dynamics, and mechanisms. J Chem Inf Model 2012; 52:617-48. [PMID: 22339582 PMCID: PMC3317594 DOI: 10.1021/ci200542m] [Citation(s) in RCA: 187] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
![]()
Metabolism of xenobiotics remains a central challenge
for the discovery
and development of drugs, cosmetics, nutritional supplements, and
agrochemicals. Metabolic transformations are frequently related to
the incidence of toxic effects that may result from the emergence
of reactive species, the systemic accumulation of metabolites, or
by induction of metabolic pathways. Experimental investigation of
the metabolism of small organic molecules is particularly resource
demanding; hence, computational methods are of considerable interest
to complement experimental approaches. This review provides a broad
overview of structure- and ligand-based computational methods for
the prediction of xenobiotic metabolism. Current computational approaches
to address xenobiotic metabolism are discussed from three major perspectives:
(i) prediction of sites of metabolism (SOMs), (ii) elucidation of
potential metabolites and their chemical structures, and (iii) prediction
of direct and indirect effects of xenobiotics on metabolizing enzymes,
where the focus is on the cytochrome P450 (CYP) superfamily of enzymes,
the cardinal xenobiotics metabolizing enzymes. For each of these domains,
a variety of approaches and their applications are systematically
reviewed, including expert systems, data mining approaches, quantitative
structure–activity relationships (QSARs), and machine learning-based
methods, pharmacophore-based algorithms, shape-focused techniques,
molecular interaction fields (MIFs), reactivity-focused techniques,
protein–ligand docking, molecular dynamics (MD) simulations,
and combinations of methods. Predictive metabolism is a developing
area, and there is still enormous potential for improvement. However,
it is clear that the combination of rapidly increasing amounts of
available ligand- and structure-related experimental data (in particular,
quantitative data) with novel and diverse simulation and modeling
approaches is accelerating the development of effective tools for
prediction of in vivo metabolism, which is reflected by the diverse
and comprehensive data sources and methods for metabolism prediction
reviewed here. This review attempts to survey the range and scope
of computational methods applied to metabolism prediction and also
to compare and contrast their applicability and performance.
Collapse
Affiliation(s)
- Johannes Kirchmair
- Unilever Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, United Kingdom
| | | | | | | | | | | | | |
Collapse
|
61
|
Shahlaei M, Fassihi A, Saghaie L, Arkan E, Madadkar-Sobhani A, Pourhossein A. Computational evaluation of some indenopyrazole derivatives as anticancer compounds; application of QSAR and docking methodologies. J Enzyme Inhib Med Chem 2011; 28:16-32. [DOI: 10.3109/14756366.2011.618991] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Mohsen Shahlaei
- Department of Medicinal Chemistry, School of Pharmacy and Isfahan Pharmaceutical Sciences Research Center, Isfahan University of Medical Sciences,
Isfahan, I.R. Iran
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kermanshah University of Medical Sciences,
Kermanshah, I.R.Iran
| | - Afshin Fassihi
- Department of Medicinal Chemistry, School of Pharmacy and Isfahan Pharmaceutical Sciences Research Center, Isfahan University of Medical Sciences,
Isfahan, I.R. Iran
| | - Lotfollah Saghaie
- Department of Medicinal Chemistry, School of Pharmacy and Isfahan Pharmaceutical Sciences Research Center, Isfahan University of Medical Sciences,
Isfahan, I.R. Iran
| | - Elham Arkan
- Department of Medical Nanotechnology, School of Advanced Medical Technologies
| | - Armin Madadkar-Sobhani
- Department of Life Sciences, Barcelona Supercomputing Center,
Edificio Nexus II, Barcelona, Spain
- Department of Bioinformatics, Institute of Biophysics and Biochemistry, University of Tehran,
Tehran, I.R.Iran
| | - Alireza Pourhossein
- Young Researchers Club, Kermanshah branch, Islamic Azad University,
Kermanshah, I.R.Iran
| |
Collapse
|
62
|
How to simulate affinities for host–guest systems lacking binding mode information: application to the liquid chromatographic separation of hexabromocyclododecane stereoisomers. J Mol Model 2011; 18:2399-408. [DOI: 10.1007/s00894-011-1239-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Accepted: 09/07/2011] [Indexed: 11/28/2022]
|
63
|
Seebeck B, Wagener M, Rarey M. From Activity Cliffs to Target-Specific Scoring Models and Pharmacophore Hypotheses. ChemMedChem 2011; 6:1630-9, 1533. [DOI: 10.1002/cmdc.201100179] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2011] [Revised: 05/27/2011] [Indexed: 11/06/2022]
|
64
|
Sushko I, Novotarskyi S, Körner R, Pandey AK, Rupp M, Teetz W, Brandmaier S, Abdelaziz A, Prokopenko VV, Tanchuk VY, Todeschini R, Varnek A, Marcou G, Ertl P, Potemkin V, Grishina M, Gasteiger J, Schwab C, Baskin II, Palyulin VA, Radchenko EV, Welsh WJ, Kholodovych V, Chekmarev D, Cherkasov A, Aires-de-Sousa J, Zhang QY, Bender A, Nigsch F, Patiny L, Williams A, Tkachenko V, Tetko IV. Online chemical modeling environment (OCHEM): web platform for data storage, model development and publishing of chemical information. J Comput Aided Mol Des 2011; 25:533-54. [PMID: 21660515 PMCID: PMC3131510 DOI: 10.1007/s10822-011-9440-2] [Citation(s) in RCA: 363] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2011] [Accepted: 05/24/2011] [Indexed: 11/25/2022]
Abstract
The Online Chemical Modeling Environment is a web-based platform that aims to automate and simplify the typical steps required for QSAR modeling. The platform consists of two major subsystems: the database of experimental measurements and the modeling framework. A user-contributed database contains a set of tools for easy input, search and modification of thousands of records. The OCHEM database is based on the wiki principle and focuses primarily on the quality and verifiability of the data. The database is tightly integrated with the modeling framework, which supports all the steps required to create a predictive model: data search, calculation and selection of a vast variety of molecular descriptors, application of machine learning methods, validation, analysis of the model and assessment of the applicability domain. As compared to other similar systems, OCHEM is not intended to re-implement the existing tools or models but rather to invite the original authors to contribute their results, make them publicly available, share them with other users and to become members of the growing research community. Our intention is to make OCHEM a widely used platform to perform the QSPR/QSAR studies online and share it with other users on the Web. The ultimate goal of OCHEM is collecting all possible chemoinformatics tools within one simple, reliable and user-friendly resource. The OCHEM is free for web users and it is available online at http://www.ochem.eu.
Collapse
Affiliation(s)
- Iurii Sushko
- eADMET GmbH, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
65
|
Structure-based quantitative structure–activity relationship modeling of estrogen receptor β-ligands. Future Med Chem 2011; 3:933-45. [DOI: 10.4155/fmc.11.49] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Background: A variety of chemotypes have been studied as estrogen receptor (ER) β-selective ligands for potential drugs against various indications, including neurodegenerative diseases. Their structure–activity relationship data and the x-ray structures of the ERβ ligand-binding domain bound with different ligands have become available. Thus, it is vitally important for future development of ERβ-selective ligands that robust quantitative structure–activity relationship (QSAR) models be built. Methods/results: We employed a newly developed structure-based QSAR method (structure-based pharmacophore keys QSAR) that utilizes both the structure–activity relationship data and the 3D structural information of ERβ, as well as a robust QSAR workflow to analyze 37 ligands. Four sets of QSAR models were obtained, among which approximately 30 models afforded high (>0.60) training-r2 and test set-R2 statistics. Conclusion: We have obtained an ensemble of predictive models of ERβ ligands that will be useful in the future discovery of novel ERβ-selective molecules.
Collapse
|
66
|
Clark RD, Norinder U. Two personal perspectives on a key issue in contemporary 3D QSAR. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2011. [DOI: 10.1002/wcms.69] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - Ulf Norinder
- AstraZeneca Research and Development, Södertälje, Sweden
| |
Collapse
|
67
|
Sotriffer C, Matter H. The Challenge of Affinity Prediction: Scoring Functions for Structure-Based Virtual Screening. METHODS AND PRINCIPLES IN MEDICINAL CHEMISTRY 2011. [DOI: 10.1002/9783527633326.ch7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
68
|
Natesan S, Wang T, Lukacova V, Bartus V, Khandelwal A, Balaz S. Rigorous treatment of multispecies multimode ligand-receptor interactions in 3D-QSAR: CoMFA analysis of thyroxine analogs binding to transthyretin. J Chem Inf Model 2011; 51:1132-50. [PMID: 21476521 DOI: 10.1021/ci200055s] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
For a rigorous analysis of the receptor-ligand binding, speciation of the ligands caused by ionization, tautomerism, covalent hydration, and dynamic stereoisomerism needs to be considered. Each species may bind in several orientations or conformations (modes), especially for flexible ligands and receptors. A thermodynamic description of the multispecies (MS), multimode (MM) binding events shows that the overall association constant is equal to the weighted sum of the sums of microscopic association constants of individual modes for each species, with the weights given by the unbound fractions of individual species. This expression is a prerequisite for a precise quantitative characterization of the ligand-receptor interactions in both structure-based and ligand-based structure-activity analyses. We have implemented the MS-MM correlation expression into the comparative molecular field analysis (CoMFA), which deduces a map of the binding site from structures and binding affinities of a ligand set, in the absence of experimental structural information on the receptor. The MS-MM CoMFA approach was applied to published data for binding to transthyretin of 28 thyroxine analogs, each forming up to four ionization species under physiological conditions. The published X-ray structures of several analogs, exhibiting multiple binding modes, served as templates for the MS-MM superposition of thyroxine analogs. Additional modes were generated for compounds with flexible alkyl substituents, to identify bound conformations. The results demonstrate that the MS-MM modification improved predictive abilities of the CoMFA models, even for the standard procedure with MS-MM selected species and modes. The predicted prevalences of individual modes and the generated receptor site model are in reasonable agreement with the available X-ray data. The calibrated model can help in the design of inhibitors of transthyretin amyloid fibril formation.
Collapse
Affiliation(s)
- Senthil Natesan
- Albany College of Pharmacy and Health Sciences , Vermont Campus, Colchester, Vermont 05446, United States
| | | | | | | | | | | |
Collapse
|
69
|
Liu Y, Jing F, Xu Y, Xie Y, Shi F, Fang H, Li M, Xu W. Design, synthesis and biological activity of thiazolidine-4-carboxylic acid derivatives as novel influenza neuraminidase inhibitors. Bioorg Med Chem 2011; 19:2342-8. [DOI: 10.1016/j.bmc.2011.02.019] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2011] [Revised: 02/10/2011] [Accepted: 02/11/2011] [Indexed: 10/18/2022]
|
70
|
Díaz L, Bujons J, Delgado A, Gutiérrez-de-Terán H, Åqvist J. Computational prediction of structure-activity relationships for the binding of aminocyclitols to β-glucocerebrosidase. J Chem Inf Model 2011; 51:601-11. [PMID: 21384831 DOI: 10.1021/ci100453a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Glucocerebrosidase (GCase, acid β-Glucosidase) hydrolyzes the sphingolipid glucosylceramide into glucose and ceramide. Mutations in this enzyme lead to a lipid metabolism disorder known as Gaucher disease. The design of competitive inhibitors of GCase is a promising field of research for the design of pharmacological chaperones as new therapeutic agents. Using a series of recently reported molecules with experimental binding affinities for GCase in the nanomolar to micromolar range, we here report an extensive theoretical analysis of their binding mode. On the basis of molecular docking, molecular dynamics, and binding free energy calculations using the linear interaction energy method (LIE), we provide details on the molecular interactions supporting ligand binding in the different families of compounds. The applicability of other computational approaches, such as the COMBINE methodology, is also investigated. The results show the robustness of the standard parametrization of the LIE method, which reproduces the experimental affinities with a mean unsigned error of 0.7 kcal/mol. Several structure-activity relationships are established using the computational models here provided, including the identification of hot spot residues in the binding site. The models derived are envisaged as important tools in ligand-design programs for GCase inhibitors.
Collapse
Affiliation(s)
- Lucía Díaz
- Research Unit on Bioactive Molecules (RUBAM), Departamento de Química Biomédica, Consejo Superior de Investigaciones Científicas, (CSIC), Instituto de Química Avanzada de Catalunya (IQAC), Barcelona, Spain
| | | | | | | | | |
Collapse
|
71
|
Liu Y, Zhang L, Gong J, Fang H, Liu A, Du G, Xu W. Design, synthesis, and biological activity of thiazole derivatives as novel influenza neuraminidase inhibitors. J Enzyme Inhib Med Chem 2010; 26:506-13. [PMID: 21143042 DOI: 10.3109/14756366.2010.534732] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A series of novel influenza neuraminidase (NA) inhibitors based on thiazole core were synthesized and evaluated for their ability to inhibit NA of influenza A virus (H(3)N(2)). All compounds were synthesized in good yields starting from commercially available 2-amino-4-thiazole-acetic ester using a suitable synthetic strategy. These compounds showed moderate inhibitory activity against influenza A NA. The most potent compound of this series is compound 4d (IC(50) = 3.43 μM), which is about 20-fold less potent than oseltamivir, and could be used to design novel influenza NA inhibitors that exhibit increased activity based on thiazole ring.
Collapse
Affiliation(s)
- Yu Liu
- Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Shandong University, Jinan, Shandong, China
| | | | | | | | | | | | | |
Collapse
|
72
|
Evaluation of a Set of C9 N-acyl Neu5Ac2en Mimetics as Viral Sialidase Selective Inhibitors. INTERNATIONAL JOURNAL OF MEDICINAL CHEMISTRY 2010; 2011:539245. [PMID: 27525119 PMCID: PMC4971745 DOI: 10.1155/2011/539245] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2010] [Revised: 11/16/2010] [Accepted: 11/16/2010] [Indexed: 11/17/2022]
Abstract
Identification of selective influenza viral sialidase inhibitors is highly desirable in order to minimize or avoid the adverse effects due to the possible inhibition of endogenous human sialidases. We recently reported the evaluation of C9 N-acyl Neu5Ac2en mimetics as probes for human sialidases. Herein, we describe the in vitro activity of the same set of C9 N-acyl Neu5Ac2en mimetics against sialidases expressed by influenza virus A/PR/8/34 (H1N1), A/Memphis/1/72 (H3N2), and A/Duck/313/78 (H5N3) strains. Compound 8 is identified as a promising starting point for the development of viral sialidase selective inhibitors. Multiple sequence alignment and molecular docking techniques are also performed to explore the plausible interaction of compound 8 with viral sialidases.
Collapse
|
73
|
Rong-Kai X, Hai-Xia L, Xiao-Ming C, Yuan-Qiang W, Yong L, Ying Y, Bo Z, Zhi-Hua L. Research Article: Quantitative Sequence-Kinetics Relationship in Antigen-Antiboby Interaction Kinetics Based on a Set of Descriptors. Chem Biol Drug Des 2010; 76:345-9. [DOI: 10.1111/j.1747-0285.2010.01022.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
74
|
Mouchlis VD, Mavromoustakos TM, Kokotos G. Molecular Docking and 3D-QSAR CoMFA Studies on Indole Inhibitors of GIIA Secreted Phospholipase A2. J Chem Inf Model 2010; 50:1589-601. [PMID: 20795712 DOI: 10.1021/ci100217k] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Varnavas D. Mouchlis
- Laboratory of Organic Chemistry, Department of Chemistry, University of Athens, Panepistimiopolis, Athens 15771, Greece
| | - Thomas M. Mavromoustakos
- Laboratory of Organic Chemistry, Department of Chemistry, University of Athens, Panepistimiopolis, Athens 15771, Greece
| | - George Kokotos
- Laboratory of Organic Chemistry, Department of Chemistry, University of Athens, Panepistimiopolis, Athens 15771, Greece
| |
Collapse
|
75
|
Zhang X, Gibbs AC, Reynolds CH, Peters MB, Westerhoff LM. Quantum mechanical pairwise decomposition analysis of protein kinase B inhibitors: validating a new tool for guiding drug design. J Chem Inf Model 2010; 50:651-61. [PMID: 20205431 PMCID: PMC2860457 DOI: 10.1021/ci9003333] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
![]()
Quantum mechanical semiempirical comparative binding energy analysis calculations have been carried out for a series of protein kinase B (PKB) inhibitors derived from fragment- and structure-based drug design. These protein−ligand complexes were selected because they represent a consistent set of experimental data that includes both crystal structures and affinities. Seven scoring functions were evaluated based on both the PM3 and the AM1 Hamiltonians. The optimal models obtained by partial least-squares analysis of the aligned poses are predictive as measured by a number of standard statistical criteria and by validation with an external data set. An algorithm has been developed that provides residue-based contributions to the overall binding affinity. These residue-based binding contributions can be plotted in heat maps so as to highlight the most important residues for ligand binding. In the case of these PKB inhibitors, the maps show that Met166, Thr97, Gly43, Glu114, Ala116, and Val50, among other residues, play an important role in determining binding affinity. The interaction energy map makes it easy to identify the residues that have the largest absolute effect on ligand binding. The structure−activity relationship (SAR) map highlights residues that are most critical to discriminating between more and less potent ligands. Taken together the interaction energy and the SAR maps provide useful insights into drug design that would be difficult to garner in any other way.
Collapse
Affiliation(s)
- Xiaohua Zhang
- QuantumBio Inc, 200 Innovation Boulevard, State College, Pennsylvania 16803 and Johnson & Johnson Pharmaceutical Research and Development, LLC, Welsh and McKean Roads, PO Box 776, Spring House, Pennsylvania 19477, USA
| | | | | | | | | |
Collapse
|
76
|
Salum LB, Valadares NF. Fragment-guided approach to incorporating structural information into a CoMFA study: BACE-1 as an example. J Comput Aided Mol Des 2010; 24:803-17. [DOI: 10.1007/s10822-010-9375-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2010] [Accepted: 07/15/2010] [Indexed: 12/27/2022]
|
77
|
Carvalho AR, Melo A. Quantum Semiempirical Energy Based (SEEB) Descriptors Performance with Benzamidine Inhibitors of Trypsin. Mol Inform 2010; 29:525-31. [DOI: 10.1002/minf.201000024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2010] [Accepted: 05/04/2010] [Indexed: 11/09/2022]
|
78
|
Das S, Krein MP, Breneman CM. Binding affinity prediction with property-encoded shape distribution signatures. J Chem Inf Model 2010; 50:298-308. [PMID: 20095526 PMCID: PMC2846646 DOI: 10.1021/ci9004139] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We report the use of the molecular signatures known as "property-encoded shape distributions" (PESD) together with standard support vector machine (SVM) techniques to produce validated models that can predict the binding affinity of a large number of protein ligand complexes. This "PESD-SVM" method uses PESD signatures that encode molecular shapes and property distributions on protein and ligand surfaces as features to build SVM models that require no subjective feature selection. A simple protocol was employed for tuning the SVM models during their development, and the results were compared to SFCscore, a regression-based method that was previously shown to perform better than 14 other scoring functions. Although the PESD-SVM method is based on only two surface property maps, the overall results were comparable. For most complexes with a dominant enthalpic contribution to binding (DeltaH/-TDeltaS > 3), a good correlation between true and predicted affinities was observed. Entropy and solvent were not considered in the present approach, and further improvement in accuracy would require accounting for these components rigorously.
Collapse
Affiliation(s)
- Sourav Das
- Department of Chemistry & Chemical Biology, Rensselaer Polytechnic Institute, 110-8th Street, Troy, NY 12180
| | - Michael P. Krein
- Department of Chemistry & Chemical Biology, Rensselaer Polytechnic Institute, 110-8th Street, Troy, NY 12180
| | - Curt M. Breneman
- Department of Chemistry & Chemical Biology / RECCR Center Rensselaer Polytechnic Institute, 110-8th Street, Center for Biotechnology and Interdisciplinary Studies, Troy, NY 12180, Phone Number: 518-276-2678, Fax Number: 518-276-4887,
| |
Collapse
|
79
|
Mouchlis VD, Mavromoustakos TM, Kokotos G. Design of new secreted phospholipase A2 inhibitors based on docking calculations by modifying the pharmacophore segments of the FPL67047XX inhibitor. J Comput Aided Mol Des 2010; 24:107-15. [DOI: 10.1007/s10822-010-9319-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2009] [Accepted: 01/21/2010] [Indexed: 10/19/2022]
|
80
|
Sippl W. 3D-QSAR – Applications, Recent Advances, and Limitations. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2010. [DOI: 10.1007/978-1-4020-9783-6_4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
|
81
|
Abia D, Bastolla U, Chacón P, Fábrega C, Gago F, Morreale A, Tramontano A. In memoriam. Proteins 2010; 78:iii-viii. [DOI: 10.1002/prot.22660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
82
|
Vijayan RSK, Bera I, Prabu M, Saha S, Ghoshal N. Combinatorial Library Enumeration and Lead Hopping using Comparative Interaction Fingerprint Analysis and Classical 2D QSAR Methods for Seeking Novel GABAA α3 Modulators. J Chem Inf Model 2009; 49:2498-511. [PMID: 19891421 DOI: 10.1021/ci900309s] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- R. S. K. Vijayan
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology (a unit of CSIR), 4, Raja S.C. Mullick Road, Kolkata-700 032, West Bengal, India and Department of Bioinformatics, West Bengal University of Technology, BF - 142 Salt Lake, Kolkata-700 064
| | - Indrani Bera
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology (a unit of CSIR), 4, Raja S.C. Mullick Road, Kolkata-700 032, West Bengal, India and Department of Bioinformatics, West Bengal University of Technology, BF - 142 Salt Lake, Kolkata-700 064
| | - M. Prabu
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology (a unit of CSIR), 4, Raja S.C. Mullick Road, Kolkata-700 032, West Bengal, India and Department of Bioinformatics, West Bengal University of Technology, BF - 142 Salt Lake, Kolkata-700 064
| | - Sangita Saha
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology (a unit of CSIR), 4, Raja S.C. Mullick Road, Kolkata-700 032, West Bengal, India and Department of Bioinformatics, West Bengal University of Technology, BF - 142 Salt Lake, Kolkata-700 064
| | - Nanda Ghoshal
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology (a unit of CSIR), 4, Raja S.C. Mullick Road, Kolkata-700 032, West Bengal, India and Department of Bioinformatics, West Bengal University of Technology, BF - 142 Salt Lake, Kolkata-700 064
| |
Collapse
|
83
|
Ajmani S, Karanam S, Kulkarni SA. Rationalizing protein-ligand interactions for PTP1B inhibitors using computational methods. Chem Biol Drug Des 2009; 74:582-95. [PMID: 19824894 DOI: 10.1111/j.1747-0285.2009.00894.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein tyrosine phosphatase 1B inhibitors were reported to have anti-diabetic properties and hence this enzyme has become interesting drug target in the recent time. Huge amount of data is available in public domain about the PTP1B inhibitors in the form of X-ray structures. This study is an attempt to transform this data into useful knowledge which can be directly used to design more effective protein tyrosine phosphatase inhibitors. In this study, we have built quantitative models for activity of co-crystallized protein tyrosine phosphatase inhibitors using two new approaches developed in our group, i.e. receptor-ligand interaction and Structure-based compound optimization, prioritization and evolution based on receptor-ligand interaction descriptors and residue-wise interaction energies as descriptors, respectively. These models have given insights into the receptor-ligand interactions essential for modulating the activity of PTP1B inhibitors. An external validation set of 22 molecules was used to test predictive power of these models on external set molecules.
Collapse
Affiliation(s)
- Subhash Ajmani
- Novalead Pharma Pvt. Ltd., Pride Purple Coronet, 1st Floor, S. No. 287, Baner Road, Pune 411045, India.
| | | | | |
Collapse
|
84
|
Henrich S, Feierberg I, Wang T, Blomberg N, Wade RC. Comparative binding energy analysis for binding affinity and target selectivity prediction. Proteins 2009; 78:135-53. [DOI: 10.1002/prot.22579] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
85
|
Gil-Redondo R, Klett J, Gago F, Morreale A. gCOMBINE: A graphical user interface to perform structure-based comparative binding energy (COMBINE) analysis on a set of ligand-receptor complexes. Proteins 2009; 78:162-72. [DOI: 10.1002/prot.22543] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
86
|
Suryanarayana S, Wang JL, Richter M, Shen Y, Tang WJ, Lushington GH, Seifert R. Distinct interactions of 2'- and 3'-O-(N-methyl)anthraniloyl-isomers of ATP and GTP with the adenylyl cyclase toxin of Bacillus anthracis, edema factor. Biochem Pharmacol 2009; 78:224-30. [PMID: 19492438 DOI: 10.1016/j.bcp.2009.04.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Anthrax disease is caused by the spore-forming bacterium, Bacillus anthracis. B. anthracis produces a calmodulin-activated adenylyl cyclase (AC) toxin, edema factor (EF). Through excessive cAMP accumulation EF disrupts host defence. In a recent study [Taha HM, Schmidt J, Göttle M, Suryanarayana S, Shen Y, Tang WJ, et al. Molecular analysis of the interaction of anthrax adenylyl cyclase toxin, edema factor, with 2'(3')-O-(N-(methyl)anthraniloyl)-substituted purine and pyrimidine nucleotides. Mol Pharmacol 2009;75:693-703] we showed that various 2'(3')-O-N-(methyl)anthraniloyl (MANT)-substituted nucleoside 5'-triphosphates are potent inhibitors (K(i) values in the 0.1-5 microM range) of purified EF. Upon interaction with calmodulin we observed efficient fluorescence resonance energy transfer (FRET) between tryptophan and tyrosine residues of EF and the MANT-group of MANT-ATP. Molecular modelling suggested that both the 2'- and 3'-MANT-isomers can bind to EF. The aim of the present study was to examine the effects of defined 2'- and 3'-MANT-isomers of ATP and GTP on EF. 3'-MANT-2'-deoxy-ATP inhibited EF more potently than 2'-MANT-3'-deoxy-ATP, whereas the opposite was the case for the corresponding GTP analogs. Calmodulin-dependent direct MANT fluorescence and FRET was much larger with 2'-MANT-3'-deoxy-ATP and 2'-MANT-3'-deoxy-GTP compared to the corresponding 3'-MANT-2'-deoxy-isomers and the 2'(3')-racemates. K(i) values of MANT-nucleotides for inhibition of catalysis correlated with K(d) values of MANT-nucleotides in FRET studies. Molecular modelling indicated different positioning of the MANT-group in 2'-MANT-3'-deoxy-ATP/GTP and 3'-MANT-2'-deoxy-ATP/GTP bound to EF. Collectively, EF interacts differentially with 2'- and 3'-MANT-isomers of ATP and GTP, indicative for conformational flexibility of the catalytic site and offering a novel approach for the development of potent and selective EF inhibitors. Moreover, our present study may serve as a general model of how to use MANT-nucleotide isomers for the analysis of the molecular mechanisms of nucleotide/protein interactions.
Collapse
|
87
|
DeVore NM, Smith BD, Wang JL, Lushington GH, Scott EE. Key residues controlling binding of diverse ligands to human cytochrome P450 2A enzymes. Drug Metab Dispos 2009; 37:1319-27. [PMID: 19251817 PMCID: PMC2683692 DOI: 10.1124/dmd.109.026765] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2009] [Accepted: 02/26/2009] [Indexed: 11/22/2022] Open
Abstract
Although the human lung cytochrome P450 2A13 (CYP2A13) and its liver counterpart cytochrome P450 2A6 (CYP2A6) are 94% identical in amino acid sequence, they metabolize a number of substrates with substantially different efficiencies. To determine differences in binding for a diverse set of cytochrome P450 2A ligands, we have measured the spectral binding affinities (K(D)) for nicotine, phenethyl isothiocyanate (PEITC), coumarin, 2'-methoxyacetophenone (MAP), and 8-methoxypsoralen. The differences in the K(D) values for CYP2A6 versus CYP2A13 ranged from 74-fold for 2'-methoxyacetophenone to 1.1-fold for coumarin, with CYP2A13 demonstrating the higher affinity. To identify active site amino acids responsible for the differences in binding of MAP, PEITC, and coumarin, 10 CYP2A13 mutant proteins were generated in which individual amino acids from the CYP2A6 active site were substituted into CYP2A13 at the corresponding position. Titrations revealed that substitutions at positions 208, 300, and 301 individually had the largest effects on ligand binding. The collective relevance of these amino acids to differential ligand selectivity was verified by evaluating binding to CYP2A6 mutant enzymes that incorporate several of the CYP2A13 amino acids at these positions. Inclusion of four CYP2A13 amino acids resulted in a CYP2A6 mutant protein (I208S/I300F/G301A/S369G) with binding affinities for MAP and PEITC much more similar to those observed for CYP2A13 than to those for CYP2A6 without altering coumarin binding. The structure-based quantitative structure-activity relationship analysis using COMBINE successfully modeled the observed mutant-ligand trends and emphasized steric roles for active site residues including four substituted amino acids and an adjacent conserved Leu(370).
Collapse
Affiliation(s)
- N M DeVore
- Department of Medicinal Chemistry, University of Kansas, Lawrence, KS 66045, USA
| | | | | | | | | |
Collapse
|
88
|
Some novel insights into the binding of oseltamivir and zanamivir to H5N1 and N9 influenza virus neuraminidases: A homology modeling and flexible docking study. JOURNAL OF THE SERBIAN CHEMICAL SOCIETY 2009. [DOI: 10.2298/jsc0901001m] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
In the context of the recent pandemic threat by the worldwide spread of H5N1 avian influenza, novel insights into the mechanism of ligand binding and interaction between various inhibitors (zanamivir - ZMV, oseltamivir - OTV, 2,3-didehydro-2-deoxy-N-acetylneuraminic acid - DANA, peramivir - PMV) and neuraminidases (NA) are of vital importance for the structure-based design of new anti-viral drugs. To address this issue, three-dimensional models of H5N1-NA and N9-NA were generated by homology modeling. Traditional residues within the active site throughout the family of NA protein structures were found to be highly conserved in H5N1-NA. A subtle variation between lipophilic and hydrophilic environments in H5N1-NA with respect to N9-NA was observed, thus shedding more light on the high resistance of some H5N1 strains to various NA inhibitors. Based on these models, an ArgusLab4/AScore flexible docking study was performed. The conformational differences between OTV bound to H5N1-NA and OTV bound to N9-NA were structurally identified and quantified. A slight difference of less than 1 kcal mol-1 between the OTV-N9 and OTV-N1 binding free energies is in agreement with the experimentally predicted free energy difference. The conformational differences between ZMV and OTV bound to either H5N1-NA or N9-NA were structurally identified. The binding free energies of the ZMV complexes, being slightly higher than those of OTV, are not in agreement with what was previously proposed using homology modeling. The differences between ZMV and OTV are suggested to be ascribed to the presence/absence of Asn166 in the active cavity of ZMV/OTV in H5N1-NA, and to the presence/absence of Ser165 in the binding site of ZMV/OTV in N9-NA. The charge distribution was evaluated using the semi-empirical AM1 method. The trends of the AM1 charges of the ZMV and OTV side chains in the complexes deviate from those previously reported.
Collapse
|
89
|
Exploring the binding of HIV-1 integrase inhibitors by comparative residue interaction analysis (CoRIA). J Mol Model 2008; 15:233-45. [DOI: 10.1007/s00894-008-0399-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2008] [Accepted: 09/06/2008] [Indexed: 11/26/2022]
|
90
|
Fratev F, Jónsdóttir SÓ, Mihaylova E, Pajeva I. Molecular Basis of Inactive B-RAFWT and B-RAFV600E Ligand Inhibition, Selectivity and Conformational Stability: An in Silico Study. Mol Pharm 2008; 6:144-57. [DOI: 10.1021/mp8001107] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Filip Fratev
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet, Building 208, DK-2800 Kongens Lyngby, Denmark, Micar Ltd., 39 Asparuh Str., 1000 Sofia, Bulgaria, and Centre of Biochemical Engineering “Ivan Daskalov”, Bl. 105 Acad G. Bontchev Str., 1113 Sofia, Bulgaria
| | - Svava Ósk Jónsdóttir
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet, Building 208, DK-2800 Kongens Lyngby, Denmark, Micar Ltd., 39 Asparuh Str., 1000 Sofia, Bulgaria, and Centre of Biochemical Engineering “Ivan Daskalov”, Bl. 105 Acad G. Bontchev Str., 1113 Sofia, Bulgaria
| | - Elina Mihaylova
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet, Building 208, DK-2800 Kongens Lyngby, Denmark, Micar Ltd., 39 Asparuh Str., 1000 Sofia, Bulgaria, and Centre of Biochemical Engineering “Ivan Daskalov”, Bl. 105 Acad G. Bontchev Str., 1113 Sofia, Bulgaria
| | - Ilza Pajeva
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet, Building 208, DK-2800 Kongens Lyngby, Denmark, Micar Ltd., 39 Asparuh Str., 1000 Sofia, Bulgaria, and Centre of Biochemical Engineering “Ivan Daskalov”, Bl. 105 Acad G. Bontchev Str., 1113 Sofia, Bulgaria
| |
Collapse
|
91
|
Mitrasinovic PM. On the structure-based design of novel inhibitors of H5N1 influenza A virus neuraminidase (NA). Biophys Chem 2008; 140:35-8. [PMID: 19117662 DOI: 10.1016/j.bpc.2008.11.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2008] [Revised: 11/12/2008] [Accepted: 11/12/2008] [Indexed: 11/18/2022]
Abstract
The structure-based design of novel H5N1 neuraminidase inhibitors is currently a research topic of vital importance owing to both a recent pandemic threat by the worldwide spread of H5N1 avian influenza and the high resistance of H5N1 virus to the most widely used commercial drug, oseltamivir-OTV (Tamiflu). A specific criterion used in this work for determining fully acceptable conformations of potential inhibitors is a previous experimental proposal of exploiting potential benefits for drug design offered by the '150-cavity' adjacent to the NA active site. Using the crystal structure of H5N1 NA (PDB ID: 2hty) as the starting point, in a set of 54 inhibitors previously proposed by modifying the side chains of oseltamivir, 4 inhibitors were identified using two different computational strategies (ArgusLab4.0.1, FlexX-E3.0.1) both to lower the binding free energy (BFE) of oseltamivir and to have partially acceptable conformations. These 4 oseltamivr structure-based analogues were found to adopt the most promising conformations by identifying the guanidinium side chain of Arg156 as a prospective partner for making polar contacts, but none of the modified 4-amino groups of oseltamivir in the 4 favorable conformations was found to make polar contacts with the guanidinium side chain of Arg156. Hence, the structures of two additional inhibitors were designed and shown to further lower the binding free energy of OTV relative to the previous 54 inhibitors. These two novel structures clearly suggest that it may be possible for a new substituent to be developed by functional modifications at position of the 4-amino group of oseltamivir in order to make polar contacts with the guanidinium side chain of Arg156, and thereby enhance the binding of a more potent inhibitor. Several standpoints of vital importance for designing novel structures of potentially more effective H5N1 NA inhibitors are established.
Collapse
Affiliation(s)
- Petar M Mitrasinovic
- Center for Multidisciplinary Studies, University of Belgrade, Kneza Viseslava 1a, 11030 Belgrade, Serbia.
| |
Collapse
|
92
|
Shadnia H, Wright JS, Anderson JM. Interaction force diagrams: new insight into ligand-receptor binding. J Comput Aided Mol Des 2008; 23:185-94. [DOI: 10.1007/s10822-008-9250-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2008] [Accepted: 10/16/2008] [Indexed: 10/21/2022]
|
93
|
Fukunishi Y, Nakamura H. A new method for in-silico drug screening and similarity search using molecular dynamics maximum volume overlap (MD-MVO) method. J Mol Graph Model 2008; 27:628-36. [PMID: 19046907 DOI: 10.1016/j.jmgm.2008.10.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2008] [Revised: 10/13/2008] [Accepted: 10/15/2008] [Indexed: 11/28/2022]
Abstract
We developed a new molecular dynamics simulation method for molecular overlapping (alignment) and ligand-based in-silico drug screening based on molecular similarity. The molecular system consists of the query compound and the other compound(s) selected from a compound library. The newly introduced intermolecular interaction between compounds is proportional to the molecular overlap instead of the van der Waals and Coulomb interactions between atoms of different molecules. This method was able to achieve both conformer generation of molecules and molecular overlapping (alignment) at the same time. After an energy minimization and following short-time MD simulation, the molecules in the system were overlapped with each other and the similarity between compounds was measured by the volume of the overlap. We applied this MD simulation method to ligand-based in-silico drug screening and found that it worked well for several targets.
Collapse
Affiliation(s)
- Yoshifumi Fukunishi
- Biomedicinal Information Research Center (BIRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-41-6 Aomi, Koto-ku, Tokyo, Japan.
| | | |
Collapse
|
94
|
Martin EJ, Sullivan DC. AutoShim: Empirically Corrected Scoring Functions for Quantitative Docking with a Crystal Structure and IC50 Training Data. J Chem Inf Model 2008; 48:861-72. [DOI: 10.1021/ci7004548] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Eric J. Martin
- Department of Computer Aided Drug Discovery, Global Discovery Chemistry, Novartis Institutes for Biomedical Research, 4560 Horton Street, Emeryville, California 94608
| | - David C. Sullivan
- Department of Computer Aided Drug Discovery, Global Discovery Chemistry, Novartis Institutes for Biomedical Research, 4560 Horton Street, Emeryville, California 94608
| |
Collapse
|
95
|
|
96
|
A comprehensive analysis of the thermodynamic events involved in ligand–receptor binding using CoRIA and its variants. J Comput Aided Mol Des 2008; 22:91-104. [DOI: 10.1007/s10822-008-9172-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2007] [Accepted: 01/05/2008] [Indexed: 10/22/2022]
|
97
|
Hillebrecht A, Klebe G. Use of 3D QSAR models for database screening: a feasibility study. J Chem Inf Model 2008; 48:384-96. [PMID: 18211050 DOI: 10.1021/ci7002945] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The applicability and scope of 3D QSAR methods (CoMFA, CoMSIA) to screen databases are examined. A protocol requiring minimal user intervention has been established to align training and test set molecules using FlexS. As model system isozymes of human carbonic anhydrase (hCA) are used, all results are exemplified studying affinity toward hCA II and selectivity between hCA I and II. The predictive power of the obtained models is assessed through prediction of 663 compounds not included in the training set and compared to 2D QSAR models derived from fragment (MACCS) or property (VSA) based descriptors. The predictive power is evaluated with respect to the following criteria: the numerical, concerning the absolute accuracy of prediction, and the categorical, characterizing the ability to assign a compound to the correct activity class.
Collapse
Affiliation(s)
- Alexander Hillebrecht
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | | |
Collapse
|
98
|
Breu B, Silber K, Gohlke H. Consensus Adaptation of Fields for Molecular Comparison (AFMoC) Models Incorporate Ligand and Receptor Conformational Variability into Tailor-made Scoring Functions. J Chem Inf Model 2007; 47:2383-400. [DOI: 10.1021/ci7002472] [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)
- Benjamin Breu
- Department of Biological Sciences, J.W. Goethe-University, Max-von-Laue-Strasse 9, 60438 Frankfurt, Germany, and Department of Pharmacy, Philipps-University, Marburg, Germany
| | - Katrin Silber
- Department of Biological Sciences, J.W. Goethe-University, Max-von-Laue-Strasse 9, 60438 Frankfurt, Germany, and Department of Pharmacy, Philipps-University, Marburg, Germany
| | - Holger Gohlke
- Department of Biological Sciences, J.W. Goethe-University, Max-von-Laue-Strasse 9, 60438 Frankfurt, Germany, and Department of Pharmacy, Philipps-University, Marburg, Germany
| |
Collapse
|
99
|
Raha K, Peters MB, Wang B, Yu N, Wollacott AM, Westerhoff LM, Merz KM. The role of quantum mechanics in structure-based drug design. Drug Discov Today 2007; 12:725-31. [PMID: 17826685 DOI: 10.1016/j.drudis.2007.07.006] [Citation(s) in RCA: 187] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Herein we will focus on the use of quantum mechanics (QM) in drug design (DD) to solve disparate problems from scoring protein-ligand poses to building QM QSAR models. Through the variational principle of QM we know that we can obtain a more accurate representation of molecular systems than classical models, and while this is not a matter of debate, it still has not been shown that the expense of QM approaches is offset by improved accuracy in DD applications. Objectively validating the improved applicability and performance of QM over classical-based models in DD will be the focus of research in the coming years along with research on the conformational sampling problem as it relates to protein-ligand complexes.
Collapse
Affiliation(s)
- Kaushik Raha
- Department of Chemistry, Quantum Theory Project, University of Florida, 2328 New Physics Building, P.O. Box 118435, Gainesville, FL 32611-8435, United States
| | | | | | | | | | | | | |
Collapse
|
100
|
Lättig J, Böhl M, Fischer P, Tischer S, Tietböhl C, Menschikowski M, Gutzeit HO, Metz P, Pisabarro MT. Mechanism of inhibition of human secretory phospholipase A2 by flavonoids: rationale for lead design. J Comput Aided Mol Des 2007; 21:473-83. [PMID: 17701137 DOI: 10.1007/s10822-007-9129-8] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2007] [Accepted: 07/09/2007] [Indexed: 11/28/2022]
Abstract
The human secretory phospholipase A2 group IIA (PLA2-IIA) is a lipolytic enzyme. Its inhibition leads to a decrease in eicosanoids levels and, thereby, to reduced inflammation. Therefore, PLA2-IIA is of high pharmacological interest in treatment of chronic diseases such as asthma and rheumatoid arthritis. Quercetin and naringenin, amongst other flavonoids, are known for their anti-inflammatory activity by modulation of enzymes of the arachidonic acid cascade. However, the mechanism by which flavonoids inhibit Phospholipase A2 (PLA2) remained unclear so far. Flavonoids are widely produced in plant tissues and, thereby, suitable targets for pharmaceutical extractions and chemical syntheses. Our work focuses on understanding the binding modes of flavonoids to PLA2, their inhibition mechanism and the rationale to modify them to obtain potent and specific inhibitors. Our computational and experimental studies focused on a set of 24 compounds including natural flavonoids and naringenin-based derivatives. Experimental results on PLA2-inhibition showed good inhibitory activity for quercetin, kaempferol, and galangin, but relatively poor for naringenin. Several naringenin derivatives were synthesized and tested for affinity and inhibitory activity improvement. 6-(1,1-dimethylallyl)naringenin revealed comparable PLA2 inhibition to quercetin-like compounds. We characterized the binding mode of these compounds and the determinants for their affinity, selectivity, and inhibitory potency. Based on our results, we suggest C(6) as the most promising position of the flavonoid scaffold to introduce chemical modifications to improve affinity, selectivity, and inhibition of PLA2-IIA by flavonoids.
Collapse
Affiliation(s)
- Jens Lättig
- Structural Bioinformatics, BIOTEC TU Dresden, Tatzberg 47-51, 01307, Dresden, Germany.
| | | | | | | | | | | | | | | | | |
Collapse
|