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Darsaraee M, Kaveh S, Mani-Varnosfaderani A, Neiband MS. General structure-activity/selectivity relationship patterns for the inhibitors of the chemokine receptors (CCR1/CCR2/CCR4/CCR5) with application for virtual screening of PubChem database. J Biomol Struct Dyn 2023:1-19. [PMID: 37599469 DOI: 10.1080/07391102.2023.2248255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 08/08/2023] [Indexed: 08/22/2023]
Abstract
CC chemokine receptors (CCRs) form a crucial subfamily of G protein-linked receptors that play a distinct role in the onset and progression of various life-threatening diseases. The main aim of this research is to derive general structure-activity relationship (SAR) patterns to describe the selectivity and activity of CCR inhibitors. To this end, a total of 7332 molecules related to the inhibition of CCR1, CCR2, CCR4, and CCR5 were collected from the Binding Database and analyzed using machine learning techniques. A diverse set of 450 molecular descriptors was calculated for each molecule, and the molecules were classified based on their therapeutic targets and activities. The variable importance in the projection (VIP) approach was used to select discriminatory molecular features, and classification models were developed using supervised Kohonen networks (SKN) and counter-propagation artificial neural networks (CPANN). The reliability and predictability of the models were estimated using 10-fold cross-validation, an external validation set, and an applicability domain approach. We were able to identify different sets of molecular descriptors for discriminating between active and inactive molecules and model the selectivity of inhibitors towards different CCRs. The sensitivities of the predictions for the external test set for the SKN models ranged from 0.827-0.873. Finally, the developed classification models were used to screen approximately 2 million random molecules from the PubChem database, with average values for areas under the receiver operating characteristic curves ranging from 0.78-0.96 for SKN models and 0.75-0.89 for CPANN models.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- M Darsaraee
- Chemometrics and Cheminformatics Laboratory, Department of Analytical Chemistry, Tarbiat Modares University, Tehran, Iran
| | - S Kaveh
- Chemometrics and Cheminformatics Laboratory, Department of Analytical Chemistry, Tarbiat Modares University, Tehran, Iran
| | - A Mani-Varnosfaderani
- Chemometrics and Cheminformatics Laboratory, Department of Analytical Chemistry, Tarbiat Modares University, Tehran, Iran
| | - M S Neiband
- Department of Chemistry, Payame Noor University (PNU), Tehran, Iran
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2
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Zapadka M, Dekowski P, Kupcewicz B. HATS5m as an Example of GETAWAY Molecular Descriptor in Assessing the Similarity/Diversity of the Structural Features of 4-Thiazolidinone. Int J Mol Sci 2022; 23:ijms23126576. [PMID: 35743020 PMCID: PMC9223869 DOI: 10.3390/ijms23126576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 04/30/2022] [Accepted: 06/10/2022] [Indexed: 11/29/2022] Open
Abstract
Among the various methods for drug design, the approach using molecular descriptors for quantitative structure–activity relationships (QSAR) bears promise for the prediction of innovative molecular structures with bespoke pharmacological activity. Despite the growing number of successful potential applications, the QSAR models often remain hard to interpret. The difficulty arises from the use of advanced chemometric or machine learning methods on the one hand, and the complexity of molecular descriptors on the other hand. Thus, there is a need to interpret molecular descriptors for identifying the features of molecules crucial for desirable activity. For example, the development of structure–activity modeling of different molecule endpoints confirmed the usefulness of H-GETAWAY (H-GEometry, Topology, and Atom-Weights AssemblY) descriptors in molecular sciences. However, compared with other 3D molecular descriptors, H-GETAWAY interpretation is much more complicated. The present study provides insights into the interpretation of the HATS5m descriptor (H-GETAWAY) concerning the molecular structures of the 4-thiazolidinone derivatives with antitrypanosomal activity. According to the published study, an increase in antitrypanosomal activity is associated with both a decrease and an increase in HATS5m (leverage-weighted autocorrelation with lag 5, weighted by atomic masses) values. The substructure-based method explored how the changes in molecular features affect the HATS5m value. Based on this approach, we proposed substituents that translate into low and high HATS5m. The detailed interpretation of H-GETAWAY descriptors requires the consideration of three elements: weighting scheme, leverages, and the Dirac delta function. Particular attention should be paid to the impact of chemical compounds’ size and shape and the leverage values of individual atoms.
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Affiliation(s)
- Mariusz Zapadka
- Department of Inorganic and Analytical Chemistry, Faculty of Pharmacy, Nicolaus Copernicus University in Toruń, Jurasza 2, 85-089 Bydgoszcz, Poland
- Correspondence: (M.Z.); (B.K.)
| | - Przemysław Dekowski
- New Technologies Department, Softmaks.pl Sp. z o.o., Kraszewskiego 1, 85-241 Bydgoszcz, Poland;
| | - Bogumiła Kupcewicz
- Department of Inorganic and Analytical Chemistry, Faculty of Pharmacy, Nicolaus Copernicus University in Toruń, Jurasza 2, 85-089 Bydgoszcz, Poland
- Correspondence: (M.Z.); (B.K.)
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3
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Nekoei M, Mohammadhosseini M, Pourbasheer E. A quantitative structure–activity relationship study on
CXL017
derivatives as effective drugs for cancer treatment. J CHIN CHEM SOC-TAIP 2021. [DOI: 10.1002/jccs.202100050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Mehdi Nekoei
- Department of Chemistry, Faculty of Basic Sciences, Shahrood Branch Islamic Azad University Shahrood Iran
| | - Majid Mohammadhosseini
- Department of Chemistry, Faculty of Basic Sciences, Shahrood Branch Islamic Azad University Shahrood Iran
| | - Eslam Pourbasheer
- Department of Chemistry, Faculty of Science University of Mohaghegh Ardabili Ardabil Iran
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4
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Zhu T, Cao Z, Singh RP, Cheng H, Chen M. In silico prediction of polyethylene-aqueous and air partition coefficients of organic contaminants using linear and nonlinear approaches. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 289:112437. [PMID: 33812149 DOI: 10.1016/j.jenvman.2021.112437] [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: 01/25/2021] [Revised: 03/16/2021] [Accepted: 03/18/2021] [Indexed: 06/12/2023]
Abstract
Low-density polyethylene (LDPE) passive sampling is very attractive for use in determining chemicals concentrations. Crucial to the measurement is the coefficient (KPE) describing partitioning between LDPE and environmental matrices. 255, 117 and 190 compounds were collected for the development of datasets in three different matrices, i.e., water, air and seawater, respectively. Further, 3 pp-LFER models and 9 QSPR models based on classical multiple linear regression (MLR) coupled with prevalent nonlinear algorithms (artificial neural network, ANN and support vector machine, SVM) were performed to predict LDPE-water (KPE-W), LDPE-air (KPE-A) and LDPE-seawater (KPE-SW) partition coefficients. These developed models have satisfying predictability (R2adj: 0.805-0.966, 0.963-0.991 and 0.817-0.941; RMSEtra: 0.233-0.565, 0.200-0.406 and 0.260-0.459) and robustness (Q2ext: 0.840-0.943, 0.968-0.984 and 0.797-0.842; RMSEext: 0.308-0.514, 0.299-0.426 and 0.407-0.462) in three datasets (water, air and seawater), respectively. In particular, the reasonable mechanism interpretations revealed that the molecular size, hydrophobicity, polarizability, ionization potential, and molecular stability were the most relevant properties, for governing chemicals partitioning between LDPE and environmental matrices. The application domains (ADs) assessed here exhibited the satisfactory applicability. As such, the derived models can act as intelligent tools to predict unknown KPE values and fill the experimental gaps, which was further beneficial for the construction of enormous and reliable database to facilitate a distinct understanding of the distribution for organic contaminants in total environment.
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Affiliation(s)
- Tengyi Zhu
- School of Environmental Science and Engineering, Yangzhou University, Yangzhou, 225127, Jiangsu, China.
| | - Zaizhi Cao
- School of Environmental Science and Engineering, Yangzhou University, Yangzhou, 225127, Jiangsu, China
| | | | - Haomiao Cheng
- School of Environmental Science and Engineering, Yangzhou University, Yangzhou, 225127, Jiangsu, China
| | - Ming Chen
- School of Civil Engineering, Southeast University, Nanjing, 210096, China
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5
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Ciura K, Fedorowicz J, Andrić F, Žuvela P, Greber KE, Baranowski P, Kawczak P, Nowakowska J, Bączek T, Sączewski J. Lipophilicity Determination of Antifungal Isoxazolo[3,4- b]pyridin-3(1 H)-ones and Their N1-Substituted Derivatives with Chromatographic and Computational Methods. Molecules 2019; 24:E4311. [PMID: 31779124 PMCID: PMC6930598 DOI: 10.3390/molecules24234311] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 11/14/2019] [Accepted: 11/21/2019] [Indexed: 11/16/2022] Open
Abstract
The lipophilicity of a molecule is a well-recognized as a crucial physicochemical factor that conditions the biological activity of a drug candidate. This study was aimed to evaluate the lipophilicity of isoxazolo[3,4-b]pyridine-3(1H)-ones and their N1-substituted derivatives, which demonstrated pronounced antifungal activities. Several methods, including reversed-phase thin layer chromatography (RP-TLC), reversed phase high-performance liquid chromatography (RP-HPLC), and micellar electrokinetic chromatography (MEKC), were employed. Furthermore, the calculated logP values were estimated using various freely and commercially available software packages and online platforms, as well as density functional theory computations (DFT). Similarities and dissimilarities between the determined lipophilicity indices were assessed using several chemometric approaches. Principal component analysis (PCA) indicated that other features beside lipophilicity affect antifungal activities of the investigated derivatives. Quantitative-structure-retention-relationship (QSRR) analysis by means of genetic algorithm-partial least squares (GA-PLS)-was implemented to rationalize the link between the physicochemical descriptors and lipophilicity. Among the studied compounds, structure 16 should be considered as the best starting structure for further studies, since it demonstrated the lowest lipophilic character within the series while retaining biological activity. Sum of ranking differences (SRD) analysis indicated that the chromatographic approach, regardless of the technique employed, should be considered as the best approach for lipophilicity assessment of isoxazolones.
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Affiliation(s)
- Krzesimir Ciura
- Department of Physical Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, Al. Gen. J. Hallera 107, 80-416 Gdańsk, Poland; (K.E.G.); (P.B.); (J.N.)
| | - Joanna Fedorowicz
- Department of Chemical Technology of Drugs, Faculty of Pharmacy, Medical University of Gdańsk, Al. Gen. J. Hallera 107, 80-416 Gdańsk, Poland;
| | - Filip Andrić
- Department of Analytical Chemistry, University of Belgrade—Faculty of Chemistry, Studentski trg 12–16, 11000 Belgrade, Serbia;
| | - Petar Žuvela
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Medical University of Gdansk, Al. Gen. J. Hallera 107, 80-416 Gdańsk, Poland; (P.Ž.); (P.K.); (T.B.)
| | - Katarzyna Ewa Greber
- Department of Physical Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, Al. Gen. J. Hallera 107, 80-416 Gdańsk, Poland; (K.E.G.); (P.B.); (J.N.)
| | - Paweł Baranowski
- Department of Physical Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, Al. Gen. J. Hallera 107, 80-416 Gdańsk, Poland; (K.E.G.); (P.B.); (J.N.)
| | - Piotr Kawczak
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Medical University of Gdansk, Al. Gen. J. Hallera 107, 80-416 Gdańsk, Poland; (P.Ž.); (P.K.); (T.B.)
| | - Joanna Nowakowska
- Department of Physical Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, Al. Gen. J. Hallera 107, 80-416 Gdańsk, Poland; (K.E.G.); (P.B.); (J.N.)
| | - Tomasz Bączek
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Medical University of Gdansk, Al. Gen. J. Hallera 107, 80-416 Gdańsk, Poland; (P.Ž.); (P.K.); (T.B.)
| | - Jarosław Sączewski
- Department of Organic Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, Al. Gen. J. Hallera 107, 80-416 Gdańsk, Poland;
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6
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Kalra S, Joshi G, Munshi A, Kumar R. Structural insights of cyclin dependent kinases: Implications in design of selective inhibitors. Eur J Med Chem 2017; 142:424-458. [PMID: 28911822 DOI: 10.1016/j.ejmech.2017.08.071] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Revised: 08/31/2017] [Accepted: 08/31/2017] [Indexed: 12/17/2022]
Abstract
There are around 20 Cyclin-dependent kinases (CDKs) known till date, and various research groups have reported their role in different types of cancer. The X-ray structures of some CDKs especially CDK2 was exploited in the past few years, and several inhibitors have been found, e.g., flavopiridol, indirubicin, roscovitine, etc., but due to the specificity issues of these inhibitors (binding to all CDKs), these were called as pan inhibitors. The revolutionary outcome of palbociclib in 2015 as CDK4/6 inhibitor added a new charm to the specific inhibitor design for CDKs. Computer-aided drug design (CADD) tools added a benefit to the design and development of new CDK inhibitors by studying the binding pattern of the inhibitors to the ATP binding domain of CDKs. Herein, we have attempted a comparative analysis of structural differences between several CDKs ATP binding sites and their inhibitor specificity by depicting the important ligand-receptor interactions for a particular CDK to be targeted. This perspective provides futuristic implications in the design of inhibitors considering the spatial features and structural insights of the specific CDK.
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Affiliation(s)
- Sourav Kalra
- Centre for Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, India
| | - Gaurav Joshi
- Centre for Pharmaceutical Sciences and Natural Products, School of Basic and Applied Sciences, Central University of Punjab, Bathinda, India
| | - Anjana Munshi
- Centre for Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, India.
| | - Raj Kumar
- Centre for Pharmaceutical Sciences and Natural Products, School of Basic and Applied Sciences, Central University of Punjab, Bathinda, India.
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7
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Toropov AA, Toropova AP, Benfenati E, Nicolotti O, Carotti A, Nesmerak K, Veselinović AM, Veselinović JB, Duchowicz PR, Bacelo D, Castro EA, Rasulev BF, Leszczynska D, Leszczynski J. QSPR/QSAR Analyses by Means of the CORAL Software. PHARMACEUTICAL SCIENCES 2017. [DOI: 10.4018/978-1-5225-1762-7.ch036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
In this chapter, the methodology of building up quantitative structure—property/activity relationships (QSPRs/QSARs)—by means of the CORAL software is described. The Monte Carlo method is the basis of this approach. Simplified Molecular Input-Line Entry System (SMILES) is used as the representation of the molecular structure. The conversion of SMILES into the molecular graph is available for QSPR/QSAR analysis using the CORAL software. The model for an endpoint is a mathematical function of the correlation weights for various features of the molecular structure. Hybrid models that are based on features extracted from both SMILES and a graph also can be built up by the CORAL software. The conceptually new ideas collected and revealed through the CORAL software are: (1) any QSPR/QSAR model is a random event; and (2) optimal descriptor can be a translator of eclectic information into an endpoint prediction.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Pablo R. Duchowicz
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas INIFTA (UNLP, CCT La Plata-CONICET), Argentina
| | | | - Eduardo A. Castro
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas INIFTA (UNLP, CCT La Plata-CONICET), Argentina
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8
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Topological sub-structural molecular design (TOPS-MODE): a useful tool to explore key fragments of human $$\mathbf{A}_{3}$$ A 3 adenosine receptor ligands. Mol Divers 2015. [DOI: 10.1007/s11030-015-9617-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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9
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IMMAN: free software for information theory-based chemometric analysis. Mol Divers 2015; 19:305-19. [DOI: 10.1007/s11030-014-9565-z] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 12/24/2014] [Indexed: 11/27/2022]
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10
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Toropov AA, Toropova AP, Benfenati E, Nicolotti O, Carotti A, Nesmerak K, Veselinović AM, Veselinović JB, Duchowicz PR, Bacelo D, Castro EA, Rasulev BF, Leszczynska D, Leszczynski J. QSPR/QSAR Analyses by Means of the CORAL Software. QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIPS IN DRUG DESIGN, PREDICTIVE TOXICOLOGY, AND RISK ASSESSMENT 2015. [DOI: 10.4018/978-1-4666-8136-1.ch015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In this chapter, the methodology of building up quantitative structure—property/activity relationships (QSPRs/QSARs)—by means of the CORAL software is described. The Monte Carlo method is the basis of this approach. Simplified Molecular Input-Line Entry System (SMILES) is used as the representation of the molecular structure. The conversion of SMILES into the molecular graph is available for QSPR/QSAR analysis using the CORAL software. The model for an endpoint is a mathematical function of the correlation weights for various features of the molecular structure. Hybrid models that are based on features extracted from both SMILES and a graph also can be built up by the CORAL software. The conceptually new ideas collected and revealed through the CORAL software are: (1) any QSPR/QSAR model is a random event; and (2) optimal descriptor can be a translator of eclectic information into an endpoint prediction.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Pablo R. Duchowicz
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas INIFTA (UNLP, CCT La Plata-CONICET), Argentina
| | | | - Eduardo A. Castro
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas INIFTA (UNLP, CCT La Plata-CONICET), Argentina
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11
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Hamzeh-Mivehroud M, Rahmani S, Feizi MAH, Dastmalchi S, Rashidi MR. In VitroandIn SilicoStudies to Explore Structural Features of Flavonoids for Aldehyde Oxidase Inhibition. Arch Pharm (Weinheim) 2014; 347:738-47. [DOI: 10.1002/ardp.201400076] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2014] [Revised: 04/30/2014] [Accepted: 05/05/2014] [Indexed: 01/10/2023]
Affiliation(s)
- Maryam Hamzeh-Mivehroud
- Biotechnology Research Center; Tabriz University of Medical Sciences; Tabriz Iran
- School of Pharmacy; Tabriz University of Medical Sciences; Tabriz Iran
| | - Seifullah Rahmani
- Department of Zoology; Faculty of Natural Science; University of Tabriz; Tabriz Iran
| | | | - Siavoush Dastmalchi
- Biotechnology Research Center; Tabriz University of Medical Sciences; Tabriz Iran
- School of Pharmacy; Tabriz University of Medical Sciences; Tabriz Iran
| | - Mohammad-Reza Rashidi
- Research Center for Pharmaceutical Nanotechnology; Tabriz University of Medical Sciences; Tabriz Iran
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12
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Structural findings of cinnolines as anti-schizophrenic PDE10A inhibitors through comparative chemometric modeling. Mol Divers 2014; 18:655-71. [PMID: 24789056 DOI: 10.1007/s11030-014-9523-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Accepted: 04/08/2014] [Indexed: 12/13/2022]
Abstract
Schizophrenia is a complex psychiatric disorder associated with the distortion of striatopallidal neurotransmission of central nervous system. Phosphodiesterase10A (PDE10A) enzyme plays crucial role in cellular signaling pathways in schizophrenia. Inhibition of this enzyme may facilitate better treatment of this disease. 2D-QSAR, HQSAR, pharmacophore mapping, molecular docking, and 3D-QSAR analyses were performed on 81 cinnoline derivatives having PDE10A inhibitory activity. 2D-QSAR models were developed by multiple linear regression and partial least square analyses using both atom based and whole molecular descriptors. The best model, having considerable internal (q(2) = 0.812) and external (R(2)(pred) = 0.691) predictabilities, demonstrated importance of atom-based topological and whole molecular E-state as well as 3D topological indices. The best HQSAR model was also found to be statistically significant (q(2) = 0.664, R(2)(pred) = 0.513) and it highlighted some important structural features. PHASE-based pharmacophore hypothesis showed the importance of three hydrogen bond acceptor and one each of ring aromatic and hydrophobic features for higher activity. 3D-QSAR CoMFA and CoMSIA models were generated on two different types of alignment procedures-(1) pharmacophore (PHASE) based and (2) docking (GLIDE) based. GLIDE-based alignment produced better results for both CoMFA (Q(2) = 0.578; R(2)(pred) = 0.841) and CoMSIA (Q(2) = 0.610; R(2)(pred) = 0.824) methods. Molecular dynamics (MDs) simulations were performed for two ligand-receptor complexes and these simulations explored some crucial factors for higher activity. These findings of MD simulations were consistent with the interpretations obtained from other methods of analyses. The current study may help in designing new PDE10A inhibitors of this class.
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13
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Fatemi MH, Moghaddam MR. Prediction of water-phosphatidylcholine membrane partition coefficient of some drugs from their molecular structures. Drug Chem Toxicol 2012; 35:381-8. [DOI: 10.3109/01480545.2011.630392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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14
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Rationalization of physicochemical characters and docking of 3-alkoxy-5-phenoxy-N-thiazolyl benzamide analogs toward glucokinase activator activity. Med Chem Res 2011. [DOI: 10.1007/s00044-011-9740-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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15
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Lather V, Fernandes MX. Comparative QSAR Analyses of Competitive CYP2C9 Inhibitors using Three-Dimensional Molecular Descriptors. Chem Biol Drug Des 2011; 78:112-23. [DOI: 10.1111/j.1747-0285.2011.01106.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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16
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Ghosh J, Lewitus DY, Chandra P, Joy A, Bushman J, Knight D, Kohn J. Computational modeling of in vitro biological responses on polymethacrylate surfaces. POLYMER 2011; 52:2650-2660. [PMID: 21779132 PMCID: PMC3138629 DOI: 10.1016/j.polymer.2011.04.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The objective of this research was to examine the capabilities of QSPR (Quantitative Structure Property Relationship) modeling to predict specific biological responses (fibrinogen adsorption, cell attachment and cell proliferation index) on thin films of different polymethacrylates. Using 33 commercially available monomers it is theoretically possible to construct a library of over 40,000 distinct polymer compositions. A subset of these polymers were synthesized and solvent cast surfaces were prepared in 96 well plates for the measurement of fibrinogen adsorption. NIH 3T3 cell attachment and proliferation index were measured on spin coated thin films of these polymers. Based on the experimental results of these polymers, separate models were built for homo-, co-, and terpolymers in the library with good correlation between experiment and predicted values. The ability to predict biological responses by simple QSPR models for large numbers of polymers has important implications in designing biomaterials for specific biological or medical applications.
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Affiliation(s)
- Jayeeta Ghosh
- New Jersey Center for Biomaterials, Rutgers, The State University of New Jersey, New Brunswick, NJ 08854-8087, United State
| | - Dan Y Lewitus
- New Jersey Center for Biomaterials, Rutgers, The State University of New Jersey, New Brunswick, NJ 08854-8087, United State
| | - Prafulla Chandra
- New Jersey Center for Biomaterials, Rutgers, The State University of New Jersey, New Brunswick, NJ 08854-8087, United State
| | - Abraham Joy
- New Jersey Center for Biomaterials, Rutgers, The State University of New Jersey, New Brunswick, NJ 08854-8087, United State
| | - Jared Bushman
- New Jersey Center for Biomaterials, Rutgers, The State University of New Jersey, New Brunswick, NJ 08854-8087, United State
| | - Doyle Knight
- Department of Mechanical and Aerospace Engineering, Rutgers, The State University of New Jersey, New Brunswick, NJ 08854-8058, United States
| | - Joachim Kohn
- New Jersey Center for Biomaterials, Rutgers, The State University of New Jersey, New Brunswick, NJ 08854-8087, United State
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17
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Docking and quantitative structure-activity relationship studies for 3-fluoro-4-(pyrrolo[2,1-f][1,2,4]triazin-4-yloxy)aniline, 3-fluoro-4-(1H-pyrrolo[2,3-b]pyridin-4-yloxy)aniline, and 4-(4-amino-2-fluorophenoxy)-2-pyridinylamine derivatives as c-Met kinase inhibitors. J Comput Aided Mol Des 2011; 25:349-69. [PMID: 21487786 DOI: 10.1007/s10822-011-9425-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2010] [Accepted: 04/03/2011] [Indexed: 01/01/2023]
Abstract
We have performed docking of 3-fluoro-4-(pyrrolo[2,1-f][1,2,4]triazin-4-yloxy)aniline (FPTA), 3-fluoro-4-(1H-pyrrolo[2,3-b]pyridin-4-yloxy)aniline (FPPA), and 4-(4-amino-2-fluorophenoxy)-2-pyridinylamine (AFPP) derivatives complexed with c-Met kinase to study the orientations and preferred active conformations of these inhibitors. The study was conducted on a selected set of 103 compounds with variations both in structure and activity. Docking helped to analyze the molecular features which contribute to a high inhibitory activity for the studied compounds. In addition, the predicted biological activities of the c-Met kinase inhibitors, measured as IC(50) values were obtained by using quantitative structure-activity relationship (QSAR) methods: Comparative molecular similarity analysis (CoMSIA) and multiple linear regression (MLR) with topological vectors. The best CoMSIA model included steric, electrostatic, hydrophobic, and hydrogen bond-donor fields; furthermore, we found a predictive model containing 2D-autocorrelation descriptors, GETAWAY descriptors (GETAWAY: Geometry, Topology and Atom-Weight AssemblY), fragment-based polar surface area (PSA), and MlogP. The statistical parameters: cross-validate correlation coefficient and the fitted correlation coefficient, validated the quality of the obtained predictive models for 76 compounds. Additionally, these models predicted adequately 25 compounds that were not included in the training set.
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Qin J, Xi L, Du J, Liu H, Yao X. QSAR studies on aminothiazole derivatives as aurora a kinase inhibitors. Chem Biol Drug Des 2010; 76:527-37. [PMID: 21040493 DOI: 10.1111/j.1747-0285.2010.01030.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Quantitative structure-activity relationship studies on 54 aminothiazole derivatives as Aurora A kinase inhibitors were performed to explore the important factors affecting their biologic activity. For 2D-quantitative structure-activity relationship study, genetic algorithm combined with multiple linear regression was used to select significant molecular descriptors. The MLR model gave squared correlation coefficient of 0.828 and squared cross-validated correlation coefficient of 0.771 for the training set compounds. Comparative molecular field analysis and comparative molecular similarity indices analysis were used to develop 3D-quantitative structure-activity relationship models. The comparative molecular field analysis model gave cross-validated correlation coefficient q² of 0.695 and non-cross-validated correlation coefficient r² of 0.977. For comparative molecular similarity indices analysis model, the corresponding q² and r² were 0.698 and 0.960, respectively. The proposed 3D-quantitative structure-activity relationship models were validated by the test set compounds not used in the modeling process, with r²(pred) values of 0.788 for comparative molecular field analysis and 0.798 for comparative molecular similarity indices analysis. The 3D contour maps suggested that further modification of the aniline group of compound 22 considering electrostatic, hydrophobic and hydrogen bond properties would influence the inhibitory activity. The results from quantitative structure-activity relationship models would be very useful to understand the structure-activity relationship of these inhibitors and to guide the further structural modification of new potential inhibitors.
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Affiliation(s)
- Jin Qin
- Department of Chemistry, Lanzhou University, Lanzhou, China School of Pharmacy, Lanzhou University, Lanzhou, China
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Borges de Melo E, Ataide Martins JP, Marinho Jorge TC, Friozi MC, Castro Ferreira MM. Multivariate QSAR study on the antimutagenic activity of flavonoids against 3-NFA on Salmonella typhimurium TA98. Eur J Med Chem 2010; 45:4562-9. [PMID: 20696502 DOI: 10.1016/j.ejmech.2010.07.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2009] [Revised: 03/29/2010] [Accepted: 07/10/2010] [Indexed: 10/19/2022]
Abstract
A quantitative structure-activity relationship (QSAR) study of twenty flavonoid derivatives with antimutagenic activity against 3-nitrofluoranthene (3-NFA) was performed by Partial Least Squares (PLS), using Ordered Predictors Selection (OPS) algorithm for variable selection. Four descriptors (PJI2, Mor27m, G1e and R4u+) were selected and a good model (n = 19; R(2) = 0.747; SEC = 0.332; PRESS(cal) = 1.768; F((2,27)) = 23.585; Q(LOO)(2) = 0.590; SEV = 0.388; PRESS(val) = 2.858; R(pred)(2) = 0.591; SEP = 0.394; ARE(pred) = 5.230%; k = 1.005; k' = 0.990; |R(02) - R'(02)| = 0.109) was built with two latent variables describing 83.410% of the original information. Leave-N-out cross validation (LNO) and y-randomization were performed in order to confirm the robustness of the model. The topological descriptors selected indicate that the antimutagenic activity against 3-NFA depends on molecular size, shape and Sanderson electronegativity of flavonoids. The proposed model may provide a better understanding of the antimutagenic activity of flavonoids and can be used as a guidance for proposition of new chemopreventive agents.
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Affiliation(s)
- Eduardo Borges de Melo
- Curso de Farmácia, Centro de Ciências Médicas e Farmacêuticas, Universidade Estadual do Oeste do Paraná - Unioeste, Cascavel, PR, Brazil
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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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21
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Design of novel antituberculosis compounds using graph-theoretical and substructural approaches. Mol Divers 2009; 13:445-58. [PMID: 19340599 DOI: 10.1007/s11030-009-9129-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2008] [Accepted: 02/16/2009] [Indexed: 10/20/2022]
Abstract
The increasing resistance of Mycobacterium tuberculosis to the existing drugs has alarmed the worldwide scientific community. In an attempt to overcome this problem, two models for the design and prediction of new antituberculosis agents were obtained. The first used a mixed approach, containing descriptors based on fragments and the topological substructural molecular design approach (TOPS-MODE) descriptors. The other model used a combination of two-dimensional (2D) and three-dimensional (3D) descriptors. A data set of 167 compounds with great structural variability, 72 of them antituberculosis agents and 95 compounds belonging to other pharmaceutical categories, was analyzed. The first model showed sensitivity, specificity, and accuracy values above 80% and the second one showed values higher than 75% for these statistical indices. Subsequently, 12 structures of imidazoles not included in this study were designed, taking into account the two models. In both cases accuracy was 100%, showing that the methodology in silico developed by us is promising for the rational design of antituberculosis drugs.
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Abstract
The development of potent and selective agonists and antagonists of adenosine receptors (ARs) has been a target of medicinal chemistry research for several decades, and recently the US Food and Drug Administration has approved Lexiscan, an adenosine derivative substituted at the 2 position, for use as a pharmacologic stress agent in radionuclide myocardial perfusion imaging. Currently, some other adenosine A(2A) receptor (A(2A)AR) agonists and antagonists are undergoing preclinical testing and clinical trials. While agonists are potent antiinflammatory agents also showing hypotensive effects, antagonists are being developed for the treatment of Parkinson's disease.However, since there are still major problems in this field, including side effects, low brain penetration (for the targeting of CNS diseases), short half-life, or lack of in vivo effects, the design and development of new AR ligands is a hot research topic.This review presents an update on the medicinal chemistry of A(2A)AR agonists and antagonists, and stresses the strong need for more selective ligands at the human A(2A)AR subtype, in particular in the case of agonists.
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Affiliation(s)
- Gloria Cristalli
- Dipartimento di Scienze Chimiche, Università di Camerino, 62032 Camerino (MC), Italy.
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Quantitative structure–retention relationships of pesticides in reversed-phase high-performance liquid chromatography based on WHIM and GETAWAY molecular descriptors. Anal Chim Acta 2008; 628:162-72. [DOI: 10.1016/j.aca.2008.09.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2008] [Revised: 09/05/2008] [Accepted: 09/08/2008] [Indexed: 11/24/2022]
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González MP, Gándara Z, Fall Y, Gómez G. Radial Distribution Function descriptors for predicting affinity for vitamin D receptor. Eur J Med Chem 2008; 43:1360-5. [DOI: 10.1016/j.ejmech.2007.10.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2007] [Revised: 10/12/2007] [Accepted: 10/15/2007] [Indexed: 10/22/2022]
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25
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Fatemi MH, Gharaghani S, Mohammadkhani S, Rezaie Z. Prediction of selectivity coefficients of univalent anions for anion-selective electrode using support vector machine. Electrochim Acta 2008. [DOI: 10.1016/j.electacta.2007.12.084] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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26
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Cruz-Monteagudo M, Borges F, Perez González M, Cordeiro MNDS. Computational modeling tools for the design of potent antimalarial bisbenzamidines: Overcoming the antimalarial potential of pentamidine. Bioorg Med Chem 2007; 15:5322-39. [PMID: 17533134 DOI: 10.1016/j.bmc.2007.05.034] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2006] [Revised: 04/24/2007] [Accepted: 05/02/2007] [Indexed: 10/23/2022]
Abstract
Malaria is nowadays a worldwide and serious problem with a significant social, economic, and human cost, mainly in developing countries. In addition, the emergence and spread of resistance to existing antimalarial therapies deteriorate the global malaria situation, and lead thus to an urgent need toward the design and discovery of new antimalarial drugs. In this work, a QSAR predictive model based on GETAWAY descriptors was developed which is able to explain with, only three variables, more than 77% of the variance in antimalarial potency and displays a good internal predictive ability (of 73.3% and 72.9% from leave-one-out cross-validation and bootstrapping analyses, respectively). The performance of the proposed model was judged against other five methodologies providing evidence of the superiority of GETAWAY descriptors in predicting the antimalarial potency of the bisbenzamidine family. Moreover, a desirability analysis based on the final QSAR model showed that to be a useful way of selecting the predictive variable level necessary to obtain potent bisbenzamidines. From the proposed model it is also possible to infer that elevated high atomic masses/polarizabilities/van der Waals volumes could play a negative/positive/positive role in the molecular interactions responsible for the desired drug conformation, which is required for the optimal binding to the macromolecular target. The results obtained point out that our final QSAR model is statistically significant and robust as well as possessing a high predictive effectiveness. Thus, the model provides a feasible and practical tool for looking for new and potent antimalarial bisbenzamidines.
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Affiliation(s)
- Maykel Cruz-Monteagudo
- Applied Chemistry Research Centre, Faculty of Chemistry and Pharmacy, Central University of Las Villas, Santa Clara, Cuba
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Helguera AM, González MP, D S Cordeiro MN, Pérez MAC. Quantitative structure carcinogenicity relationship for detecting structural alerts in nitroso-compounds. Toxicol Appl Pharmacol 2007; 221:189-202. [PMID: 17477948 DOI: 10.1016/j.taap.2007.02.021] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2007] [Revised: 02/16/2007] [Accepted: 02/21/2007] [Indexed: 02/01/2023]
Abstract
Prevention of environmentally induced cancers is a major health problem of which solutions depend on the rapid and accurate screening of potential chemical hazards. Lately, theoretical approaches such as the one proposed here - Quantitative Structure-Activity Relationship (QSAR) - are increasingly used for assessing the risks of environmental chemicals, since they can markedly reduce costs, avoid animal testing, and speed up policy decisions. This paper reports a QSAR study based on the Topological Substructural Molecular Design (TOPS-MODE) approach, aiming at predicting the rodent carcinogenicity of a set of nitroso-compounds selected from the Carcinogenic Potency Data Base (CPDB). The set comprises nitrosoureas (14 chemicals), N-nitrosamines (18 chemicals) C-nitroso-compounds (1 chemical), nitrosourethane (1 chemical) and nitrosoguanidine (1 chemical), which have been bioassayed in male rat using gavage as the route of administration. Here we are especially concerned in gathering the role of both parameters on the carcinogenic activity of this family of compounds. First, the regression model was derived, upon removal of one identified nitrosamine outlier, and was able to account for more than 84% of the variance in the experimental activity. Second, the TOPS-MODE approach afforded the bond contributions -- expressed as fragment contributions to the carcinogenic activity -- that can be interpreted and provide tools for better understanding the mechanisms of carcinogenesis. Finally, and most importantly, we demonstrate the potentialities of this approach towards the recognition of structural alerts for carcinogenicity predictions.
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Affiliation(s)
- Aliuska Morales Helguera
- Department of Chemistry, Faculty of Chemistry and Pharmacy, Central University of Las Villas, Santa Clara, 54830, Villa Clara, Cuba
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Saíz-Urra L, González MP, Fall Y, Gómez G. Quantitative structure–activity relationship studies of HIV-1 integrase inhibition. 1. GETAWAY descriptors. Eur J Med Chem 2007; 42:64-70. [PMID: 17030481 DOI: 10.1016/j.ejmech.2006.08.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2006] [Revised: 08/11/2006] [Accepted: 08/14/2006] [Indexed: 11/21/2022]
Abstract
The GEometry, Topology, and Atom-Weights AssemblY (GETAWAY) approach has been applied to the study of the HIV-1 integrase inhibition of 172 compounds that belong to 11 different chemistry families. A model able to describe more than 68.5% of the variance in the experimental activity was developed with the use of the mentioned approach. In contrast, none of the five different approaches, including the use of Randić Molecular Profiles, Geometrical, RDF, 3D-MORSE and WHIM descriptors was able to explain more than 62.4% of the variance in the mentioned property with the same number of variables in the equation. Finally, after extracting five compounds considered by us as outliers the model was able to describe more than 72.5% of the variance in the experimental activity.
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Affiliation(s)
- Liane Saíz-Urra
- Chemical Bioactive Center, Central University of Las Villas, Santa Clara, Villa Clara, CP 54830, Cuba
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González MP, Puente M, Fall Y, Gómez G. In silico studies using Radial Distribution Function approach for predicting affinity of 1 alpha,25-dihydroxyvitamin D(3) analogues for Vitamin D receptor. Steroids 2006; 71:510-27. [PMID: 16566955 DOI: 10.1016/j.steroids.2006.02.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2005] [Revised: 02/02/2006] [Accepted: 02/04/2006] [Indexed: 01/28/2023]
Abstract
The Radial Distribution Function (RDF) approach has been applied to the study of the chick intestinal VDR affinity of 49 Vitamin D analogues. A model able to describe more than 77.5% of the variance in the experimental activity was developed with the use of the mentioned approach. In contrast, none of four different approaches, including the use of Topological, BCUT, Randić molecular profiles and Geometrical descriptors were able to explain more than 55% of the variance in the mentioned property, with the same number of variables in the equation.
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