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Sahin K, Saripinar E, Durdagi S. Combined 4D-QSAR and target-based approaches for the determination of bioactive Isatin derivatives. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2021; 32:769-792. [PMID: 34530651 DOI: 10.1080/1062936x.2021.1971760] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 08/19/2021] [Indexed: 06/13/2023]
Abstract
The hybrid method of the Electron-Conformational Genetic Algorithm (EC-GA) was used to determine the pharmacophore groups and to estimate anticancer activity in isatin derivatives using a robust 4D-QSAR software (EMRE). To build the model, each compound is represented by a set of conformers rather than a single conformation. The Electron Conformational Matrix of Congruity (ECMC) is composed via EMRE software. Electron Conformational Submatrix of Activity (ECSA) was calculated by the comparison of these matrices. Genetic algorithm was used to select important variables to predict theoretical activity. The model with the best seven parameters produced satisfactory results. The E statistics technique was applied to the generated EC-GA model to evaluate the individual contribution of each of the descriptors on biological activity. The r2 and q2 values of the training set compounds were found to be 0.95 and 0.93, respectively. Because no previous 4D-QSAR studies on isatin derivatives have been conducted, this study is important in the development of new isatin derivatives. In this study, 27 isatin derivatives whose activities were estimated using the hybrid EC-GA method were also investigated through molecular docking and molecular dynamics simulations for their BCL-2 inhibitory activity.
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Affiliation(s)
- K Sahin
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey
| | - E Saripinar
- Faculty of Science, Department of Chemistry, Erciyes University, Kayseri, Turkey
| | - S Durdagi
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey
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2
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Two Decades of 4D-QSAR: A Dying Art or Staging a Comeback? Int J Mol Sci 2021; 22:ijms22105212. [PMID: 34069090 PMCID: PMC8156896 DOI: 10.3390/ijms22105212] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/11/2021] [Accepted: 05/12/2021] [Indexed: 01/01/2023] Open
Abstract
A key question confronting computational chemists concerns the preferable ligand geometry that fits complementarily into the receptor pocket. Typically, the postulated ‘bioactive’ 3D ligand conformation is constructed as a ‘sophisticated guess’ (unnecessarily geometry-optimized) mirroring the pharmacophore hypothesis—sometimes based on an erroneous prerequisite. Hence, 4D-QSAR scheme and its ‘dialects’ have been practically implemented as higher level of model abstraction that allows the examination of the multiple molecular conformation, orientation and protonation representation, respectively. Nearly a quarter of a century has passed since the eminent work of Hopfinger appeared on the stage; therefore the natural question occurs whether 4D-QSAR approach is still appealing to the scientific community? With no intention to be comprehensive, a review of the current state of art in the field of receptor-independent (RI) and receptor-dependent (RD) 4D-QSAR methodology is provided with a brief examination of the ‘mainstream’ algorithms. In fact, a myriad of 4D-QSAR methods have been implemented and applied practically for a diverse range of molecules. It seems that, 4D-QSAR approach has been experiencing a promising renaissance of interests that might be fuelled by the rising power of the graphics processing unit (GPU) clusters applied to full-atom MD-based simulations of the protein-ligand complexes.
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3
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Sahin K, Saripinar E. A novel hybrid method named electron conformational genetic algorithm as a 4D QSAR investigation to calculate the biological activity of the tetrahydrodibenzazosines. J Comput Chem 2020; 41:1091-1104. [PMID: 32058616 DOI: 10.1002/jcc.26154] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 12/18/2019] [Accepted: 12/18/2019] [Indexed: 11/11/2022]
Abstract
To understand the structure-activity correlation of a group of tetrahydrodibenzazocines as inhibitors of 17β-hydroxysteroid dehydrogenase type 3, we have performed a combined genetic algorithm (GA) and four-dimensional quantitative structure-activity relationship (4D-QSAR) modeling study. The computed electronic and geometry structure descriptors were regulated as a matrix and named as electron-conformational matrix of contiguity (ECMC). A chemical property-based pharmacophore model was developed for series of tetrahydrodibenzazocines by EMRE software package. GA was employed to choose an optimal combination of parameters. A model has been developed for estimating anticancer activity quantitatively. All QSAR models were established with 40 compounds (training set), then they were considered for selective capability with additional nine compounds (test set). A statistically valid 4D-QSAR ( R training 2 = 0.856 , R test 2 = 0.851 and q2 = 0.650) with good external set prediction was obtained.
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Affiliation(s)
- Kader Sahin
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey
| | - Emin Saripinar
- Science Faculty, Department of Chemistry, Erciyes University, Kayseri, Turkey
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4
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Martínez-Santiago O, Marrero-Ponce Y, Vivas-Reyes R, Ugarriza MEO, Hurtado-Rodríguez E, Martínez-López Y, Torres FJ, Zambrano CH, Pham-The H. Higher-Order and Mixed Discrete Derivatives such as a Novel Graph- Theoretical Invariant for Generating New Molecular Descriptors. Curr Top Med Chem 2019; 19:944-956. [PMID: 31074367 DOI: 10.2174/1568026619666190510093651] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 02/22/2019] [Accepted: 03/27/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND Recently, some authors have defined new molecular descriptors (MDs) based on the use of the Graph Discrete Derivative, known as Graph Derivative Indices (GDI). This new approach about discrete derivatives over various elements from a graph takes as outset the formation of subgraphs. Previously, these definitions were extended into the chemical context (N-tuples) and interpreted in structural/physicalchemical terms as well as applied into the description of several endpoints, with good results. OBJECTIVE A generalization of GDIs using the definitions of Higher Order and Mixed Derivative for molecular graphs is proposed as a generalization of the previous works, allowing the generation of a new family of MDs. METHODS An extension of the previously defined GDIs is presented, and for this purpose, the concept of Higher Order Derivatives and Mixed Derivatives is introduced. These novel approaches to obtaining MDs based on the concepts of discrete derivatives (finite difference) of the molecular graphs use the elements of the hypermatrices conceived from 12 different ways (12 events) of fragmenting the molecular structures. The result of applying the higher order and mixed GDIs over any molecular structure allows finding Local Vertex Invariants (LOVIs) for atom-pairs, for atoms-pairs-pairs and so on. All new families of GDIs are implemented in a computational software denominated DIVATI (acronym for Discrete DeriVAtive Type Indices), a module of KeysFinder Framework in TOMOCOMD-CARDD system. RESULTS QSAR modeling of the biological activity (Log 1/K) of 31 steroids reveals that the GDIs obtained using the higher order and mixed GDIs approaches yield slightly higher performance compared to previously reported approaches based on the duplex, triplex and quadruplex matrix. In fact, the statistical parameters for models obtained with the higher-order and mixed GDI method are superior to those reported in the literature by using other 0-3D QSAR methods. CONCLUSION It can be suggested that the higher-order and mixed GDIs, appear as a promissory tool in QSAR/QSPRs, similarity/dissimilarity analysis and virtual screening studies.
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Affiliation(s)
- Oscar Martínez-Santiago
- Universidad de San Buenaventura - Cartagena - Facultad de Ciencias de la Salud - Grupo de Investigación Microbiología & Ambiente (GIMA) - Calle Real de Ternera, Diagonal 32, No. 30-966, Cartagena, Código postal: 1300 10 - Colombia.,Universidad San Francisco de Quito (USFQ), Grupo de Medicina Molecular y Traslacional (MeM&T), Colegio de Ciencias de la Salud (COCSA), Escuela de Medicina, Edificio de Especialidades Médicas, Av. Interoceánica Km 12 ½ -Cumbayá, Quito 170157, Ecuador.,Universidad San Francisco de Quito (USFQ), Instituto de Simulación Computacional (ISC-USFQ), Diego de Robles y vía Interoceánica, 17-1200-841, Quito, Ecuador and Departamento de Química, Facultad de Ciencias Aplicadas, Universidad de Camagüey, 74650, Camagüey, Cuba
| | - Yovani Marrero-Ponce
- Universidad San Francisco de Quito (USFQ), Grupo de Medicina Molecular y Traslacional (MeM&T), Colegio de Ciencias de la Salud (COCSA), Escuela de Medicina, Edificio de Especialidades Médicas, Av. Interoceánica Km 12 ½ -Cumbayá, Quito 170157, Ecuador.,Universidad San Francisco de Quito (USFQ), Instituto de Simulación Computacional (ISC-USFQ), Diego de Robles y vía Interoceánica, 17-1200-841, Quito, Ecuador and Departamento de Química, Facultad de Ciencias Aplicadas, Universidad de Camagüey, 74650, Camagüey, Cuba
| | - Ricardo Vivas-Reyes
- Grupo Ginumed. Fundacion Universitaria Rafael Nuñez. Facultad de Salud. Programa de Medicina. Cartagena-Colombia.,Grupo CipTec, Fundacion Universitaria Tecnologico de Comfenalco, Facultad de Ingenierias, Fundacion Universitaria Tecnologico Comfenalco - Cartagena, Cr 44 D N 30A, 91, Cartagena, Bolivar, Colombia.,Group of Quantum and Theoretical Chemistry, Faculty of Exacts and Naturals Sciences, University of Cartagena, Cartagena de Indias, Bolívar, 130001, Colombia
| | - Mauricio E O Ugarriza
- Universidad de San Buenaventura - Cartagena - Facultad de Ciencias de la Salud - Grupo de Investigación Microbiología & Ambiente (GIMA) - Calle Real de Ternera, Diagonal 32, No. 30-966, Cartagena, Código postal: 1300 10 - Colombia
| | - Elízabeth Hurtado-Rodríguez
- Universidad de San Buenaventura - Cartagena - Facultad de Ciencias de la Salud - Grupo de Investigación Microbiología & Ambiente (GIMA) - Calle Real de Ternera, Diagonal 32, No. 30-966, Cartagena, Código postal: 1300 10 - Colombia
| | - Yoan Martínez-López
- Universidad San Francisco de Quito (USFQ), Grupo de Medicina Molecular y Traslacional (MeM&T), Colegio de Ciencias de la Salud (COCSA), Escuela de Medicina, Edificio de Especialidades Médicas, Av. Interoceánica Km 12 ½ -Cumbayá, Quito 170157, Ecuador.,Grupo de Investigación de Inteligencia Artificial (AIRES), Facultad de Informática, Universidad de Camagüey, Camagüey, Cuba
| | - F Javier Torres
- Universidad San Francisco de Quito (USFQ), Instituto de Simulación Computacional (ISC-USFQ), Diego de Robles y vía Interoceánica, 17-1200-841, Quito, Ecuador and Departamento de Química, Facultad de Ciencias Aplicadas, Universidad de Camagüey, 74650, Camagüey, Cuba.,Universidad San Francisco de Quito, Grupo de Química Computacional y Teórica (QCTUSFQ), Departamento de Ingeniería Química, Diego de Robles y Vía Interoceánica, Quito, 17-1200-841, Ecuador
| | - Cesar H Zambrano
- Universidad San Francisco de Quito (USFQ), Instituto de Simulación Computacional (ISC-USFQ), Diego de Robles y vía Interoceánica, 17-1200-841, Quito, Ecuador and Departamento de Química, Facultad de Ciencias Aplicadas, Universidad de Camagüey, 74650, Camagüey, Cuba.,Universidad San Francisco de Quito, Grupo de Química Computacional y Teórica (QCTUSFQ), Departamento de Ingeniería Química, Diego de Robles y Vía Interoceánica, Quito, 17-1200-841, Ecuador
| | - Hai Pham-The
- Department of Pharmaceutical Chemistry, Hanoi University of Pharmacy, 13-15 Le Thanh Tong, Hoan Kiem, Hanoi, Vietnam
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5
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Luque Ruiz I, Gómez-Nieto MÁ. Robust QSAR prediction models for volume of distribution at steady state in humans using relative distance measurements. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2018; 29:529-550. [PMID: 30044137 DOI: 10.1080/1062936x.2018.1494038] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 06/25/2018] [Indexed: 06/08/2023]
Abstract
The building of quantitative structure-activity relationship (QSAR) models for the in silico prediction of volume distribution for drugs at steady-state levels is vital for the selection of potential drugs at the synthesis stage. Using molecular descriptor matrixes, some regression models presenting low accuracy have been proposed, mainly due to the difficulty of compiling an appropriate dataset and the lack of information on dataset representation. In this paper, we use a benchmark dataset of very diverse drugs for the development of predictive models for volume distribution based on the use of relative distance matrixes as the input data to QSAR algorithms. Support vector machine, complex tree, bagged tree and Gaussian process regression algorithms were tested for fingerprint, similarity and relative distance matrixes used as input data, and the results of the built models were compared. Relative distance matrixes generated robust regression models in the training and external validation stages performed using cross-validation, obtaining values for correlation coefficient, bias, slope and root-mean-square error close to the ideal. Relative distance matrixes were also used for the design of classification models, obtaining excellent results with values of accuracy and area under receiver operating characteristic (AUC) close to 100%.
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Affiliation(s)
- I Luque Ruiz
- a Department of Computing and Numerical Analysis , University of Córdoba, Campus de Rabanales , Albert Einstein building, E-14071 , Córdoba , Spain
| | - M Á Gómez-Nieto
- a Department of Computing and Numerical Analysis , University of Córdoba, Campus de Rabanales , Albert Einstein building, E-14071 , Córdoba , Spain
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6
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Ruiz IL, Gómez-Nieto MÁ. Advantages of Relative versus Absolute Data for the Development of Quantitative Structure–Activity Relationship Classification Models. J Chem Inf Model 2017; 57:2776-2788. [DOI: 10.1021/acs.jcim.7b00492] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Irene Luque Ruiz
- Department of Computing and
Numerical
Analysis, University of Córdoba, Albert Einstein building, Campus de Rabanales, E-14071, Córdoba, Spain
| | - Miguel Ángel Gómez-Nieto
- Department of Computing and
Numerical
Analysis, University of Córdoba, Albert Einstein building, Campus de Rabanales, E-14071, Córdoba, Spain
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7
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Martin YC, Abagyan R, Ferenczy GG, Gillet VJ, Oprea TI, Ulander J, Winkler D, Zefirov NS. Glossary of terms used in computational drug design, part II (IUPAC Recommendations 2015). PURE APPL CHEM 2016. [DOI: 10.1515/pac-2012-1204] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractComputational drug design is a rapidly changing field that plays an increasingly important role in medicinal chemistry. Since the publication of the first glossary in 1997, substantial changes have occurred in both medicinal chemistry and computational drug design. This has resulted in the use of many new terms and the consequent necessity to update the previous glossary. For this purpose a Working Party of eight experts was assembled. They produced explanatory definitions of more than 150 new and revised terms.
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Affiliation(s)
| | - Ruben Abagyan
- 2UCSD Skaggs School of Pharmacy and Pharmaceutical Sciences, La Jolla, CA 92093, USA
| | - György G. Ferenczy
- 3Department of Biophysics and Radiation Biology, Semmelweis University Budapest, 1444 Budapest, Pf 263, Hungary
| | - Val J. Gillet
- 4Information School, University of Sheffield, Sheffield S1 4DP, UK
| | - Tudor I. Oprea
- 5School of Medicine, Department of Internal Medicine, University of New Mexico, Albuquerque, NM 87131 USA
| | - Johan Ulander
- 6AstraZeneca, CVGI Medicinal Chemistry, Molndal, S43183 Sweden
| | - David Winkler
- 7CSIRO, Materials Science and Engineering, Clayton VIC 3169, Australia
| | - Nicolai S. Zefirov
- 8Department of Chemistry, Moscow State University (MSU), Moscow, 119899, Russia
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8
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Khedkar VM, Coutinho EC. CoRILISA: A Local Similarity Based Receptor Dependent QSAR Method. J Chem Inf Model 2015; 55:194-205. [DOI: 10.1021/ci5006367] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Vijay M. Khedkar
- Department of Pharmaceutical Chemistry, Bombay College of Pharmacy, Kalina, Santacruz (E), Mumbai 400098, India
| | - Evans C. Coutinho
- Department of Pharmaceutical Chemistry, Bombay College of Pharmacy, Kalina, Santacruz (E), Mumbai 400098, India
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9
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Khedkar VM, Joseph J, Pissurlenkar R, Saran A, Coutinho EC. How good are ensembles in improving QSAR models? The case with eCoRIA. J Biomol Struct Dyn 2014; 33:749-69. [DOI: 10.1080/07391102.2014.909744] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Vijay M. Khedkar
- Department of Pharmaceutical Chemistry, Bombay College of Pharmacy, Kalina, Santacruz (E), Mumbai 400098, India
| | - Jose Joseph
- Department of Pharmaceutical Chemistry, Bombay College of Pharmacy, Kalina, Santacruz (E), Mumbai 400098, India
| | - Raghuvir Pissurlenkar
- Department of Pharmaceutical Chemistry, Bombay College of Pharmacy, Kalina, Santacruz (E), Mumbai 400098, India
| | - Anil Saran
- Department of Pharmaceutical Chemistry, Bombay College of Pharmacy, Kalina, Santacruz (E), Mumbai 400098, India
| | - Evans C. Coutinho
- Department of Pharmaceutical Chemistry, Bombay College of Pharmacy, Kalina, Santacruz (E), Mumbai 400098, India
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Abstract
AbstractAbstract The CORAL software (http://www.insilico.eu/coral/) has been examined as a tool for modeling anti-HIV-1 activity by quantitative structure — activity relationships (QSAR) for three different sets: (i) TIBO derivatives (n=82) (ii) anti-HIV-1 activity of 2-amino-6-arylsulfonylbenzonitriles and their congeners (n=64), and (iii) the measured binding affinity for fullerene-based HIV-1 PR inhibitors (n=48). A new global invariant ATOMPAIR of the molecular structure which can be calculated with the simplified molecular input line entry system (SMILES) was studied. The ATOMPAIR is an indicator of the joint presence of pairs of chemical elements (F, Cl, Br, N, O, S, and P) and three types of bonds (double covalent bond, triple covalent bond, and stereo chemical bond). Six random splits into sub-training, calibration, and test set were examined for each set. For the three aforementioned sets, the use of ATOMPAIR in the modeling process improves the predictive potential of the models for six random splits. Graphical abstract
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Varnek A, Baskin I. Machine learning methods for property prediction in chemoinformatics: Quo Vadis? J Chem Inf Model 2012; 52:1413-37. [PMID: 22582859 DOI: 10.1021/ci200409x] [Citation(s) in RCA: 148] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
This paper is focused on modern approaches to machine learning, most of which are as yet used infrequently or not at all in chemoinformatics. Machine learning methods are characterized in terms of the "modes of statistical inference" and "modeling levels" nomenclature and by considering different facets of the modeling with respect to input/ouput matching, data types, models duality, and models inference. Particular attention is paid to new approaches and concepts that may provide efficient solutions of common problems in chemoinformatics: improvement of predictive performance of structure-property (activity) models, generation of structures possessing desirable properties, model applicability domain, modeling of properties with functional endpoints (e.g., phase diagrams and dose-response curves), and accounting for multiple molecular species (e.g., conformers or tautomers).
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Affiliation(s)
- Alexandre Varnek
- Laboratoire d'Infochimie, UMR 7177 CNRS, Université de Strasbourg, 4, rue B. Pascal, Strasbourg 67000, France.
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Shen MY, Su BH, Esposito EX, Hopfinger AJ, Tseng YJ. A Comprehensive Support Vector Machine Binary hERG Classification Model Based on Extensive but Biased End Point hERG Data Sets. Chem Res Toxicol 2011; 24:934-49. [DOI: 10.1021/tx200099j] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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13
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Yanmaz E, Sarıpınar E, Şahin K, Geçen N, Çopur F. 4D-QSAR analysis and pharmacophore modeling: electron conformational-genetic algorithm approach for penicillins. Bioorg Med Chem 2011; 19:2199-210. [PMID: 21419636 DOI: 10.1016/j.bmc.2011.02.035] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2010] [Revised: 02/01/2011] [Accepted: 02/19/2011] [Indexed: 11/30/2022]
Abstract
4D-QSAR studies were performed on a series of 87 penicillin analogues using the electron conformational-genetic algorithm (EC-GA) method. In this EC-based method, each conformation of the molecular system is described by a matrix (ECMC) with both electron structural parameters and interatomic distances as matrix elements. Multiple comparisons of these matrices within given tolerances for high active and low active penicillin compounds allow one to separate a smaller number of matrix elements (ECSA) which represent the pharmacophore groups. The effect of conformations was investigated building model 1 and 2 based on ensemble of conformers and single conformer, respectively. GA was used to select the most important descriptors and to predict the theoretical activity of the training (74 compounds) and test (13 compounds, commercial penicillins) sets. The model 1 for training and test sets obtained by optimum 12 parameters gave more satisfactory results (R(training)(2)=0.861, SE(training)=0.044, R(test)(2)=0.892, SE(test)=0.099, q(2)=0.702, q(ext1)(2)=0.777 and q(ext2)(2)=0.733) than model 2 (R(training)(2)=0.774, SE(training)=0.056, R(test)(2)=0.840, SE(test)=0.121, q(2)=0.514, q(ext1)(2)=0.641 and q(ext2)(2)=0.570). To estimate the individual influence of each of the molecular descriptors on biological activity, the E statistics technique was applied to the derived EC-GA model.
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Affiliation(s)
- Ersin Yanmaz
- Balıkesir University, Altınoluk Vacational College, Department of Chemistry, Balıkesir, Turkey
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14
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On the information expressed in enzyme structure: more lessons from ribonuclease A. Mol Divers 2011; 15:769-79. [PMID: 21347658 DOI: 10.1007/s11030-011-9307-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2010] [Accepted: 02/05/2011] [Indexed: 01/17/2023]
Abstract
Brownian computations were directed at Ribonuclease A (RNase A) and variants in folded states so as to quantify information of the statistical type at the atom/covalent bond level. This advanced the research reported in this journal last year on the information properties of enzyme primary structure. Brownian computation data are illustrated for a sixteen-member library. The results identify signature traits that distinguish the folded wild type (WT) molecule from variants. The distinctions are explainable in terms of correlated information and dispersion energy. The Brownian tools used for this study can be directed at other protein families (e.g., kinases, isomerases, etc.) in rapid screening, QSAR, and design applications.
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Abstract
Computer-aided drug design (CADD) methodologies have made great advances and contributed significantly to the discovery and/or optimization of many clinically used drugs in recent years. CADD tools have likewise been applied to the discovery of inhibitors of HIV-1 integrase, a difficult and worthwhile target for the development of efficient anti-HIV drugs. This article reviews the application of CADD tools, including pharmacophore search, quantitative structure-activity relationships, model building of integrase complexed with viral DNA and quantum-chemical studies in the discovery of HIV-1 integrase inhibitors. Different structurally diverse integrase inhibitors have been identified by, or with significant help from, various CADD tools.
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Affiliation(s)
- Chenzhong Liao
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS, NCI-Frederick, 376 Boyles Street, Frederick, MD 21702, USA
| | - Marc C Nicklaus
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS, NCI-Frederick, 376 Boyles Street, Frederick, MD 21702, USA
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Andrade CH, Pasqualoto KFM, Ferreira EI, Hopfinger AJ. 4D-QSAR: perspectives in drug design. Molecules 2010; 15:3281-94. [PMID: 20657478 PMCID: PMC6263259 DOI: 10.3390/molecules15053281] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2010] [Revised: 03/30/2010] [Accepted: 04/06/2010] [Indexed: 12/05/2022] Open
Abstract
Drug design is a process driven by innovation and technological breakthroughs involving a combination of advanced experimental and computational methods. A broad variety of medicinal chemistry approaches can be used for the identification of hits, generation of leads, as well as to accelerate the optimization of leads into drug candidates. The quantitative structure–activity relationship (QSAR) formalisms are among the most important strategies that can be applied for the successful design new molecules. This review provides a comprehensive review on the evolution and current status of 4D-QSAR, highlighting present challenges and new opportunities in drug design.
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Affiliation(s)
- Carolina H. Andrade
- Laboratory of Molecular Modeling, Faculty of Pharmacy, Federal University of Goiás, 1ª Av. c/ Praça Universitária, S/N., Goiânia, Goiás, 74605-220, Brazil
- College of Pharmacy, MSC09 5360, 1 University of New Mexico, Albuquerque, New Mexico 87131-0001, USA; E-Mail: (A.J.H.)
- Author to whom correspondence should be addressed; E-Mail:
| | - Kerly F. M. Pasqualoto
- Faculty of Pharmaceutical Sciences, Av. Prof. Lineu Prestes, 580, University of Sao Paulo, Sao Paulo, 05508-900, Brazil; E-Mails: (K.F.M.P.); (E.I.F.)
| | - Elizabeth I. Ferreira
- Faculty of Pharmaceutical Sciences, Av. Prof. Lineu Prestes, 580, University of Sao Paulo, Sao Paulo, 05508-900, Brazil; E-Mails: (K.F.M.P.); (E.I.F.)
| | - Anton J. Hopfinger
- College of Pharmacy, MSC09 5360, 1 University of New Mexico, Albuquerque, New Mexico 87131-0001, USA; E-Mail: (A.J.H.)
- The Chem21 Group, Inc., 17870 Wilson Drive. Lake Forest, IL 60045, USA
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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]
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Consonni V, Todeschini R. Molecular Descriptors. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2010. [DOI: 10.1007/978-1-4020-9783-6_3] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Verma J, Malde A, Khedkar S, Iyer R, Coutinho E. Local Indices for Similarity Analysis (LISA)—A 3D-QSAR Formalism Based on Local Molecular Similarity. J Chem Inf Model 2009; 49:2695-707. [DOI: 10.1021/ci900224u] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jitender Verma
- Department of Pharmaceutical Chemistry, Bombay College of Pharmacy, Kalina, Santacruz (E), Mumbai 400 098, India, and Spring Bank Pharmaceuticals, Inc., 113 Cedar Street, Milford, Massachusetts 01757
| | - Alpeshkumar Malde
- Department of Pharmaceutical Chemistry, Bombay College of Pharmacy, Kalina, Santacruz (E), Mumbai 400 098, India, and Spring Bank Pharmaceuticals, Inc., 113 Cedar Street, Milford, Massachusetts 01757
| | - Santosh Khedkar
- Department of Pharmaceutical Chemistry, Bombay College of Pharmacy, Kalina, Santacruz (E), Mumbai 400 098, India, and Spring Bank Pharmaceuticals, Inc., 113 Cedar Street, Milford, Massachusetts 01757
| | - Radhakrishnan Iyer
- Department of Pharmaceutical Chemistry, Bombay College of Pharmacy, Kalina, Santacruz (E), Mumbai 400 098, India, and Spring Bank Pharmaceuticals, Inc., 113 Cedar Street, Milford, Massachusetts 01757
| | - Evans Coutinho
- Department of Pharmaceutical Chemistry, Bombay College of Pharmacy, Kalina, Santacruz (E), Mumbai 400 098, India, and Spring Bank Pharmaceuticals, Inc., 113 Cedar Street, Milford, Massachusetts 01757
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Thipnate P, Liu J, Hannongbua S, Hopfinger AJ. 3D pharmacophore mapping using 4D QSAR analysis for the cytotoxicity of lamellarins against human hormone-dependent T47D breast cancer cells. J Chem Inf Model 2009; 49:2312-22. [PMID: 19799437 PMCID: PMC2798151 DOI: 10.1021/ci9002427] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
4D quantitative structure-activity relationship (QSAR) and 3D pharmacophore models were built and investigated for cytotoxicity using a training set of 25 lamellarins against human hormone dependent T47D breast cancer cells. Receptor-independent (RI) 4D QSAR models were first constructed from the exploration of eight possible receptor-binding alignments for the entire training set. Since the training set is small (25 compounds), the generality of the 4D QSAR paradigm was then exploited to devise a strategy to maximize the extraction of binding information from the training set and to also permit virtual screening of diverse lamellarin chemistry. 4D QSAR models were sought for only six of the most potent lamellarins of the training set as well as another subset composed of lamellarins with constrained ranges in molecular weight and lipophilicity. This overall modeling strategy has permitted maximizing 3D pharmacophore information from this small set of structurally complex lamellarins that can be used to drive future analog synthesis and the selection of alternate scaffolds. Overall, it was found that the formation of an intermolecular hydrogen bond and the hydrophobic interactions for substituents on the E ring most modulate the cytotoxicity against T47D breast cancer cells. Hydrophobic substitutions on the F-ring can also enhance cytotoxic potency. A complementary high-throughput virtual screen to the 3D pharmacophore models, a 4D fingerprint QSAR model, was constructed using absolute molecular similarity. This 4D fingerprint virtual high-throughput screen permits a larger range of chemistry diversity to be assayed than with the 4D QSAR models. The optimized 4D QSAR 3D pharmacophore model has a leave-one-out cross-correlation value of xv-r2 = 0.947, while the optimized 4D fingerprint virtual screening model has a value of xv-r2 = 0.719. This work reveals that it is possible to develop significant QSAR, 3D pharmacophore, and virtual screening models for a small set of lamellarins showing cytotoxic behavior in breast cancer screens that can guide future drug development based upon lamellarin chemistry.
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Affiliation(s)
- Poonsiri Thipnate
- Department of Chemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
- Center of Nanotechnology KU, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Jianzhong Liu
- College of Pharmacy, MSC09 5360, 1 University of New Mexico, Albuquerque, New Mexico 87131-000, USA
- The Chem21 Group, Incorporated, 1780 Wilson Drive, Lake Forest, IL 60045
| | - Supa Hannongbua
- Department of Chemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
- Center of Nanotechnology KU, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - A. J. Hopfinger
- College of Pharmacy, MSC09 5360, 1 University of New Mexico, Albuquerque, New Mexico 87131-000, USA
- The Chem21 Group, Incorporated, 1780 Wilson Drive, Lake Forest, IL 60045
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21
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Categorical QSAR models for skin sensitization based on local lymph node assay measures and both ground and excited state 4D-fingerprint descriptors. J Comput Aided Mol Des 2008; 22:345-66. [DOI: 10.1007/s10822-008-9190-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2007] [Accepted: 01/30/2008] [Indexed: 10/22/2022]
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Santos-Filho OA, Hopfinger AJ. Combined 4D‐Fingerprint and Clustering Based Membrane‐Interaction QSAR Analyses for Constructing Consensus Caco‐2 Cell Permeation Virtual Screens. J Pharm Sci 2008; 97:566-83. [PMID: 17696143 DOI: 10.1002/jps.21086] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A set of 30 structurally diverse molecules, for which Caco-2 cell permeation coefficients were determined, formed the training set for construction of Caco-2 cell permeation models based upon membrane-interaction (MI) QSAR analysis and a new QSAR method called 4D-fingerprint QSAR analysis. The descriptor terms of the 4D-fingerprints equation are molecular similarity eigenvalues, and this set of descriptors is being evaluated as a potential "universal" QSAR descriptor set. The 4D-fingerprint model suggests that Caco-2 cell permeation is governed by the spatial distribution of hydrogen bonding and nonpolar groups over the molecular shape of a molecule. Moreover, a complementary resampling of the original Caco-2 cell permeation training set, followed by the construction of several "clustered" MI-QSAR models, led to a consensus model consistent in interpretation with the 4D-fingerprint model.
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Affiliation(s)
- Osvaldo A Santos-Filho
- Division of Infectious Diseases, Faculty of Medicine, University of British Columbia, 2733 Heather Street, Vancouver, British Columbia, Canada.
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Li Y, Pan D, Liu J, Kern PS, Gerberick GF, Hopfinger AJ, Tseng YJ. Categorical QSAR Models for Skin Sensitization based upon Local Lymph Node Assay Classification Measures Part 2: 4D-Fingerprint Three-State and Two-2-State Logistic Regression Models. Toxicol Sci 2007; 99:532-44. [PMID: 17675333 DOI: 10.1093/toxsci/kfm185] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Three and four state categorical quantitative structure-activity relationship (QSAR) models for skin sensitization have been constructed using data from the murine Local Lymph Node Assay studies. These are the same data we previously used to build two-state (sensitizer, nonsensitizer) QSAR models (Li et al., 2007, Chem. Res. Toxicol. 20, 114-128). 4D-fingerprint descriptors derived from the 4D-molecular similarity paradigm are used to generate these models. A training set of 196 and a test set of 22 structurally diverse compounds were used in this study. Logistic regression, and partial least square coupled logistic regression were used to build the models. The three-state QSAR model gives a classification accuracy of 73.4% for the training set and 63.6% for the test set, while the random average value of classification accuracy for any three-state data set is 33.3%. The two-2-state [four categories in total] QSAR model gives a classification accuracy of 83.2% for the training set and 54.6% for the test set, while the random average value of classification accuracy for any two-2-state data set is 25%. An analysis of the skin-sensitization models developed in this study, as well as the two-state QSAR models developed in our previous analysis, suggests that the "moderate" sensitizers may be the main source of limited model accuracy.
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Affiliation(s)
- Yi Li
- Laboratory of Molecular Modeling and Design (MC 781), College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612-7231, USA
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Li Y, Tseng YJ, Pan D, Liu J, Kern PS, Gerberick GF, Hopfinger AJ. 4D-fingerprint categorical QSAR models for skin sensitization based on the classification of local lymph node assay measures. Chem Res Toxicol 2007; 20:114-28. [PMID: 17226934 PMCID: PMC2553001 DOI: 10.1021/tx6002535] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Currently, the only validated methods to identify skin sensitization effects are in vivo models, such as the local lymph node assay (LLNA) and guinea pig studies. There is a tremendous need, in particular due to novel legislation, to develop animal alternatives, for eaxample, quantitative structure-activity relationship (QSAR) models. Here, QSAR models for skin sensitization using LLNA data have been constructed. The descriptors used to generate these models are derived from the 4D-molecular similarity paradigm and are referred to as universal 4D-fingerprints. A training set of 132 structurally diverse compounds and a test set of 15 structurally diverse compounds were used in this study. The statistical methodologies used to build the models are logistic regression (LR) and partial least-square coupled logistic regression (PLS-LR), which prove to be effective tools for studying skin sensitization measures expressed in the two categorical terms of sensitizer and non-sensitizer. QSAR models with low values of the Hosmer-Lemeshow goodness-of-fit statistic, X(2)HL, are significant and predictive. For the training set, the cross-validated prediction accuracy of the logistic regression models ranges from 77.3% to 78.0%, whereas that of the PLS-logistic regression models ranges from 87.1% to 89.4%. For the test set, the prediction accuracy of logistic regression models ranges from 80.0% to 86.7%, whereas that of the PLS-logistic regression models ranges from 73.3% to 80.0%. The QSAR models are made up of 4D-fingerprints related to aromatic atoms, hydrogen bond acceptors, and negatively partially charged atoms.
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Affiliation(s)
- Yi Li
- Laboratory of Molecular Modeling and Design (MC 781), College of Pharmacy, University of Illinois at Chicago, 833 South Wood Street, Chicago, IL 60612-7231
| | - Yufeng J. Tseng
- The Chem21 Group, Inc., 1780 Wilson Drive, Lake Forest, IL 60045
- Dept. of Computer Science and Information Engineering, National Taiwan University, No.1 Sec. 4, Roosevelt Road, Taipei, Taiwan 106
| | - Dahua Pan
- Laboratory of Molecular Modeling and Design (MC 781), College of Pharmacy, University of Illinois at Chicago, 833 South Wood Street, Chicago, IL 60612-7231
| | - Jianzhong Liu
- College of Pharmacy, MSC09 5360, 1 University of New Mexico, Albuquerque, NM 87131-0001
- The Chem21 Group, Inc., 1780 Wilson Drive, Lake Forest, IL 60045
| | - Petra S. Kern
- Procter& Gamble Eurocor, Temselaan 100, B-1853 Strombeek-Bever, Belgium
| | - G. Frank Gerberick
- The Procter & Gamble Company, Miami Valley Innovation Center, P.O. Box 538707, Cincinnati, OH 45253-8707
| | - Anton J. Hopfinger
- College of Pharmacy, MSC09 5360, 1 University of New Mexico, Albuquerque, NM 87131-0001
- The Chem21 Group, Inc., 1780 Wilson Drive, Lake Forest, IL 60045
- Corresponding Author: Voice: 505.272.8474, Fax: 505.272.0704,
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Liu J, Yang L, Li Y, Pan D, Hopfinger AJ. Constructing plasma protein binding model based on a combination of cluster analysis and 4D-fingerprint molecular similarity analyses. Bioorg Med Chem 2006; 14:611-21. [PMID: 16214346 DOI: 10.1016/j.bmc.2005.08.035] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2005] [Revised: 08/22/2005] [Accepted: 08/22/2005] [Indexed: 12/01/2022]
Abstract
Based on 2D-connectivity molecular similarity and cluster analyses, a dataset for HSA binding is divided into the training set and the test set. 4D-fingerprint similarity measures were applied to this dataset. Four different predictive schemes (SM, SA, SR, and SC) were applied to the test set based on the similarity measures of each compound to the compounds in the training set. The first algorithmic scheme (SM), which only takes the most similar compound in the training set into consideration, predicts the binding affinity of a test compound. This scheme has relatively poor predictivity based on 4D-fingerprint similarity analyses. The other three algorithmic schemes (SM, SR, and SC), which assign a weighting coefficient to each of the top-ten most similar training set compounds, have reasonable predictivity of a test set. The algorithmic scheme which categorizes the most similar compounds into different weighted clusters predicts the test set best. The 4D-fingerprints provide 36 different individual IPE/IPE type molecular similarity measures. Further investigation shows that the NP/HA, HS/HA, and HA/HA IPE/IPE type measures predict the test set well. Moreover, these three IPE/IPE type similarity measures are very similar to one another for the particular training and test sets investigated. The 4D-fingerprints have relatively high predictivity for this particular dataset.
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Affiliation(s)
- Jianzhong Liu
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA.
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Senese CL, Duca J, Pan D, Hopfinger AJ, Tseng YJ. 4D-fingerprints, universal QSAR and QSPR descriptors. ACTA ACUST UNITED AC 2005; 44:1526-39. [PMID: 15446810 DOI: 10.1021/ci049898s] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An elusive goal in the field of chemoinformatics and molecular modeling has been the generation of a set of descriptors that, once calculated for a molecule, may be used in a wide variety of applications. Since such universal descriptors are generated free from external constraints, they are inherently independent of the data set in which they are employed. The realization of a set of universal descriptors would significantly streamline such chemoinformatics tasks as virtual high-throughout screening (VHTS) and toxicity profiling. The current study reports the derivation and validation of a potential set of universal descriptors, referred to as the 4D-fingerprints. The 4D-fingerprints are derived from the 4D-molecular similarity analysis. To evaluate the applicability of the 4D-fingerprints as universal descriptors, they are used to generate descriptive QSAR models for 5 independent training sets. Each of the training sets has been analyzed previously by several varying QSAR methods, and the results of the models generated using the 4D-fingerprints are compared to the results of the previous QSAR analyses. It was found that the models generated using the 4D-fingerprints are comparable in quality, based on statistical measures of fit and test set prediction, to the previously reported models for the other QSAR methods. This finding is particularly significant considering the 4D-fingerprints are generated independent of external constraints such as alignment, while the QSAR methods used for comparison all require an alignment analysis.
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Affiliation(s)
- Craig L Senese
- Laboratory of Molecular Modeling and Design (MC 781), College of Pharmacy, The University of Illinois at Chicago, 833 South Wood Street, Chicago, Illinois 60612-7231, USA
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Liu J, Yang L, Li Y, Pan D, Hopfinger AJ. Prediction of plasma protein binding of drugs using Kier–Hall valence connectivity indices and 4D-fingerprint molecular similarity analyses. J Comput Aided Mol Des 2005; 19:567-83. [PMID: 16267692 DOI: 10.1007/s10822-005-9012-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2005] [Accepted: 08/02/2005] [Indexed: 10/25/2022]
Abstract
A 115 compound dataset for HSA binding is divided into the training set and the test set based on molecular similarity and cluster analyses. Both Kier-Hall valence connectivity indices and 4D-fingerprint similarity measures were applied to this dataset. Four different predictive schemes (SM, SA, SR, SC) were applied to the test set based on the similarity measures of each compound to the compounds in the training set. The first algorithmic scheme (SM) predicts the binding affinity of a test compound using only the most similar training set compound's binding affinity. This scheme has relatively poor predictivity based both on Kier-Hall valence connectivity indices similarity measures and 4D-fingerprints similarity analyses. The other three algorithmic schemes (SM SR, SC), which assign a weighting coefficient to each of the top-ten most similar training set compounds, have reasonable predictivity of a test set. The algorithmic scheme which categorizes the most similar compounds into different weighted clusters predicts the test set best. The 4D-fingerprints provide 36 different individual IPE/IPE type molecular similarity measures. This study supports that some types of similarity measures are highly similar to one another for this dataset. Both the Kier-Hall valence connectivity indices similarity measures and the 4D-fingerprints have nearly same predictivity for this particular dataset.
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Affiliation(s)
- Jianzhong Liu
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA.
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Liu J, Pan D, Tseng Y, Hopfinger AJ. 4D-QSAR analysis of a series of antifungal p450 inhibitors and 3D-pharmacophore comparisons as a function of alignment. ACTA ACUST UNITED AC 2004; 43:2170-9. [PMID: 14632469 DOI: 10.1021/ci034142z] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A training set of 55 antifungal p450 analogue inhibitors was used to construct receptor-independent four-dimensional quantitative structure-activity relationship (RI 4D-QSAR) models. Ten different alignments were used to build the models, and one alignment yields a significantly better model than the other alignments. Two different methodologies were used to measure the similarity of the best 4D-QSAR models of each alignment. One method compares the residual of fit between pairs of models using the cross-correlation coefficient of their residuals of fit as a similarity measure. The other method compares the spatial distributions of the IPE types (3D-pharmacophores) of pairs of 4D-QSAR models from different alignments. Optimum models from several different alignments have nearly the same correlation coefficients, r(2), and cross-validation correlation coefficients, xv-r(2), yet the 3D-pharmacophores of these models are very different from one another. The highest 3D-pharmacophore similarity correlation coefficient between any pair of 4D-QSAR models from the 10 alignments considered is only 0.216. However, the best 4D-QSAR models of each alignment do contain some proximate common pharmacorphore sites. A test set of 10 compounds was used to validate the predictivity of the best 4D-QSAR models of each alignment. The "best" model from the 10 alignments has the highest predictivity. The inferred active sites mapped out by the 4D-QSAR models suggest that hydrogen bond interactions are not prevalent when this class of P450 analogue inhibitors binds to the receptor active site. This feature of the 4D-QSAR models is in agreement with the crystal structure results that indicate no ligand-receptor hydrogen bonds are formed.
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Affiliation(s)
- Jianzhong Liu
- Laboratory of Molecular Modeling and Design (M/C 781), College of Pharmacy, The University of Illinois at Chicago, 833 South Wood Street, Chicago, Illinois 60612-7231, USA
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Abstract
High-throughput and virtual screening are important components of modern drug discovery research. Typically, these screening technologies are considered distinct approaches, as one is experimental and the other is theoretical in nature. However, given their similar tasks and goals, these approaches are much more complementary to each other than often thought. Various statistical, informatics and filtering methods have recently been introduced to foster the integration of experimental and in silico screening and maximize their output in drug discovery. Although many of these ideas and efforts have not yet proceeded much beyond the conceptual level, there are several success stories and good indications that early-stage drug discovery will benefit greatly from a more unified and knowledge-based approach to biological screening, despite the many technical advances towards even higher throughput that are made in the screening arena.
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Affiliation(s)
- Jürgen Bajorath
- Department of Computer-Aided Drug Discovery, Albany Molecular Research, Inc., Bothell Research Center, 18804 North Creek Parkway, Bothell, Washington 98011, USA.
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Abstract
This article reviews current achievements in the field of chemoinformatics and their impact on modern drug discovery processes. The main data mining approaches used in cheminformatics, such as descriptor computations, structural similarity matrices, and classification algorithms, are outlined. The applications of cheminformatics in drug discovery, such as compound selection, virtual library generation, virtual high throughput screening, HTS data mining, and in silico ADMET are discussed. At the conclusion, future directions of chemoinformatics are suggested.
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Affiliation(s)
- Jun Xu
- Author to whom correspondence should be addressed; e-mail:
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