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Hachim ME, Sadik K, Byadi S, Aboulmouhajir A. Electronic investigation and spectroscopic analysis using DFT with the long-range dispersion correction on the six lowest conformers of 2.2.3-trimethyl pentane. J Mol Model 2020; 26:168. [PMID: 32514768 DOI: 10.1007/s00894-020-04430-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 05/26/2020] [Indexed: 10/24/2022]
Abstract
The conformational stability and internal rotation barriers, HOMO-LUMO gap and related properties, molecular static polarizability and hyperpolarizability parameters, and the NBO delocalization energies associated with the internal charge transfer (ICT) of 2.2.3-trimethylpentane in the ground state were carried out taking into account the long range dispersion correction through CAM-B3LYP and WB97XD levels at aug-cc-pvtz basis set. The six lowest conformations were differentiated by a deep and multiple spectroscopic investigation. The ultraviolet-visible (UV-Vis) absorption bands are assigned using molecular orbital data obtained by TD-WB97XD/aug-cc-pvtz calculations, and carbon 13C NMR signal peaks have been assigned using GIAO-WB97XD/aug-cc-pvtz method. In addition, the normal mode calculations of the most and less stable conformers using a scaled force field in terms of non-redundant local symmetry coordinates have been confronted to the experimental vibrational spectra temperature dependency.
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Affiliation(s)
- Mouhi Eddine Hachim
- Team of Molecular Modelling and Spectroscopy, Sciences Faculty, University of Chouaib Doukkali, El Jadida, Morocco
| | - Karima Sadik
- Team of Molecular Modelling and Spectroscopy, Sciences Faculty, University of Chouaib Doukkali, El Jadida, Morocco
| | - Said Byadi
- Organic synthesis, Extraction and Valorization laboratory, Team of Extraction, Spectroscopy and Valorization, Sciences Faculty of Ain Chock, University of Hassan II, Casablanca, Morocco
| | - Aziz Aboulmouhajir
- Team of Molecular Modelling and Spectroscopy, Sciences Faculty, University of Chouaib Doukkali, El Jadida, Morocco. .,Organic synthesis, Extraction and Valorization laboratory, Team of Extraction, Spectroscopy and Valorization, Sciences Faculty of Ain Chock, University of Hassan II, Casablanca, Morocco.
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2
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Affiliation(s)
- Hagit Sason
- Faculty of Biomedical Engineering Technion – Israel Institute of Technology Haifa Israel
| | - Yosi Shamay
- Faculty of Biomedical Engineering Technion – Israel Institute of Technology Haifa Israel
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3
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Applying Discriminant and Cluster Analyses to Separate Allergenic from Non-allergenic Proteins. OPEN CHEM 2019. [DOI: 10.1515/chem-2019-0045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
AbstractAs a result of increased healthcare requirements and the introduction of genetically modified foods, the problem of allergies is becoming a growing health problem. The concept of allergies has prompted the use of new methods such as genomics and proteomics to uncover the nature of allergies. In the present study, a selection of 1400 food proteins was analysed by PLS-DA (Partial Least Square-based Discriminant Analysis) after suitable transformation of structural parameters into uniform vectors. Then, the resulting strings of different length were converted into vectors with equal length by Auto and Cross-Covariance (ACC) analysis. Hierarchical and non-hierarchical (K-means) Cluster Analysis (CA) was also performed in order to reach a certain level of separation within a small training set of plant proteins (16 allergenic and 16 non-allergenic) using a new three-dimensional descriptor based on surface protein properties in combination with amino acid hydrophobicity scales. The novelty of the approach in protein differentiation into allergenic and non-allergenic classes is described in the article.The general goal of the present study was to show the effectiveness of a traditional chemometric method for classification (PLS–DA) and the options of Cluster Analysis (CA) to separate by multivariate statistical methods allergenic from non-allergenic proteins.
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Takagi K, Nishikawa Y, Shimizu K, Nobuke K, Yamakado R, Sugimoto S, Inai Y. Synthesis and Structure of Optically Active Oligo( N
-substituted- m
-benzamide)s Bearing a Bithiophene Chromophore on the Benzene Ring. MACROMOL CHEM PHYS 2018. [DOI: 10.1002/macp.201800298] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Koji Takagi
- Prof. K. Takagi, Y. Nishikawa, K. Shimizu, K. Nobuke, Dr. R. Yamakado , S. Sugimoto, Prof. Y. Inai; Graduate School of Engineering; Nagoya Institute of Technology, Gokiso, Showa; Nagoya 466-8555 Japan
| | - Yuma Nishikawa
- Prof. K. Takagi, Y. Nishikawa, K. Shimizu, K. Nobuke, Dr. R. Yamakado , S. Sugimoto, Prof. Y. Inai; Graduate School of Engineering; Nagoya Institute of Technology, Gokiso, Showa; Nagoya 466-8555 Japan
| | - Kana Shimizu
- Prof. K. Takagi, Y. Nishikawa, K. Shimizu, K. Nobuke, Dr. R. Yamakado , S. Sugimoto, Prof. Y. Inai; Graduate School of Engineering; Nagoya Institute of Technology, Gokiso, Showa; Nagoya 466-8555 Japan
| | - Katsuya Nobuke
- Prof. K. Takagi, Y. Nishikawa, K. Shimizu, K. Nobuke, Dr. R. Yamakado , S. Sugimoto, Prof. Y. Inai; Graduate School of Engineering; Nagoya Institute of Technology, Gokiso, Showa; Nagoya 466-8555 Japan
| | - Ryohei Yamakado
- Prof. K. Takagi, Y. Nishikawa, K. Shimizu, K. Nobuke, Dr. R. Yamakado , S. Sugimoto, Prof. Y. Inai; Graduate School of Engineering; Nagoya Institute of Technology, Gokiso, Showa; Nagoya 466-8555 Japan
| | - Shinri Sugimoto
- Prof. K. Takagi, Y. Nishikawa, K. Shimizu, K. Nobuke, Dr. R. Yamakado , S. Sugimoto, Prof. Y. Inai; Graduate School of Engineering; Nagoya Institute of Technology, Gokiso, Showa; Nagoya 466-8555 Japan
| | - Yoshihito Inai
- Prof. K. Takagi, Y. Nishikawa, K. Shimizu, K. Nobuke, Dr. R. Yamakado , S. Sugimoto, Prof. Y. Inai; Graduate School of Engineering; Nagoya Institute of Technology, Gokiso, Showa; Nagoya 466-8555 Japan
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5
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Daunes S, Yardley V, Croft SL, D'Silva C. Antiprotozoal glutathione derivatives with flagellar membrane binding activity against T. brucei rhodesiense. Bioorg Med Chem 2016; 25:1329-1340. [PMID: 28131508 DOI: 10.1016/j.bmc.2016.12.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2016] [Revised: 12/05/2016] [Accepted: 12/10/2016] [Indexed: 12/16/2022]
Abstract
A new series of N-substituted S-(2,4-dinitrophenyl)glutathione dibutyl diesters were synthesized to improve in vitro anti-protozoal activity against the pathogenic parasites Trypanosoma brucei rhodesiense, Trypanosoma cruzi and Leishmania donovani. The results obtained indicate that N-substituents enhance the inhibitory properties of glutathione diesters whilst showing reduced toxicity against KB cells as in the cases of compounds 5, 9, 10, 16, 18 and 19. We suggest that the interaction of N-substituted S-(2,4-dinitrophenyl) glutathione dibutyl diesters with T. b. brucei occurs mainly by weak hydrophobic interactions such as London and van der Waals forces. A QSAR study indicated that the inhibitory activity of the peptide is associated negatively with the average number of C atoms, NC and positively to SZX, the ZX shadow a geometric descriptor related to molecular size and orientation of the compound. HPLC-UV studies in conjunction with optical microscopy indicate that the observed selectivity of inhibition of these compounds against bloodstream form T. b. brucei parasites in comparison to L. donovani under the same conditions is due to intracellular uptake via endocytosis in the flagellar pocket.
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Affiliation(s)
- Sylvie Daunes
- School of Chemistry and Environmental Sciences, The Manchester Metropolitan University, Faculty of Science and Engineering, John Dalton Building, Chester Street, Manchester M1 5GD, UK
| | - Vanessa Yardley
- Department of Immunology and Infection, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Simon L Croft
- Department of Immunology and Infection, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Claudius D'Silva
- School of Chemistry and Environmental Sciences, The Manchester Metropolitan University, Faculty of Science and Engineering, John Dalton Building, Chester Street, Manchester M1 5GD, UK; School of Chemistry, Central University of Rajasthan, Bandar Sindari, Jaipur-Ajmer Highway (Rajasthan), India.
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6
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Mohamed A, Nguyen CH, Mamitsuka H. Current status and prospects of computational resources for natural product dereplication: a review. Brief Bioinform 2015; 17:309-21. [PMID: 26153512 DOI: 10.1093/bib/bbv042] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Indexed: 01/08/2023] Open
Abstract
Research in natural products has always enhanced drug discovery by providing new and unique chemical compounds. However, recently, drug discovery from natural products is slowed down by the increasing chance of re-isolating known compounds. Rapid identification of previously isolated compounds in an automated manner, called dereplication, steers researchers toward novel findings, thereby reducing the time and effort for identifying new drug leads. Dereplication identifies compounds by comparing processed experimental data with those of known compounds, and so, diverse computational resources such as databases and tools to process and compare compound data are necessary. Automating the dereplication process through the integration of computational resources has always been an aspired goal of natural product researchers. To increase the utilization of current computational resources for natural products, we first provide an overview of the dereplication process, and then list useful resources, categorizing into databases, methods and software tools and further explaining them from a dereplication perspective. Finally, we discuss the current challenges to automating dereplication and proposed solutions.
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Judycka-Proma U, Bober L, Gajewicz A, Puzyn T, Błażejowski J. Chemometric analysis of correlations between electronic absorption characteristics and structural and/or physicochemical parameters for ampholytic substances of biological and pharmaceutical relevance. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 138:700-710. [PMID: 25544186 DOI: 10.1016/j.saa.2014.11.067] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Revised: 11/05/2014] [Accepted: 11/22/2014] [Indexed: 06/04/2023]
Abstract
Forty ampholytic compounds of biological and pharmaceutical relevance were subjected to chemometric analysis based on unsupervised and supervised learning algorithms. This enabled relations to be found between empirical spectral characteristics derived from electronic absorption data and structural and physicochemical parameters predicted by quantum chemistry methods or phenomenological relationships based on additivity rules. It was found that the energies of long wavelength absorption bands are correlated through multiparametric linear relationships with parameters reflecting the bulkiness features of the absorbing molecules as well as their nucleophilicity and electrophilicity. These dependences enable the quantitative analysis of spectral features of the compounds, as well as a comparison of their similarities and certain pharmaceutical and biological features. Three QSPR models to predict the energies of long-wavelength absorption in buffers with pH=2.5 and pH=7.0, as well as in methanol, were developed and validated in this study. These models can be further used to predict the long-wavelength absorption energies of untested substances (if they are structurally similar to the training compounds).
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Affiliation(s)
- U Judycka-Proma
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland; Research Laboratory, Polpharma S.A., Pelplińska 19, 80-200 Starogard Gdański, Poland
| | - L Bober
- Research Laboratory, Polpharma S.A., Pelplińska 19, 80-200 Starogard Gdański, Poland
| | - A Gajewicz
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - T Puzyn
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland.
| | - J Błażejowski
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland.
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Chaudret R, Kiss CF, Subramanian L. Prediction of absorption wavelengths using a combination of semi-empirical quantum mechanics simulations and quantitative structure–property relationship modeling approaches. J Photochem Photobiol A Chem 2015. [DOI: 10.1016/j.jphotochem.2014.11.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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9
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Beheshti A, Riahi S, Ganjali MR, Norouzi P. Highlighting and trying to overcome a serious drawback with qspr studies; data collection in different experimental conditions (mixed-QSPR). J Comput Chem 2012; 33:732-47. [DOI: 10.1002/jcc.22892] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Revised: 10/03/2011] [Accepted: 10/18/2011] [Indexed: 11/08/2022]
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10
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Ghasemi JB, Salahinejad M, Rofouei MK. Review of the quantitative structure–activity relationship modelling methods on estimation of formation constants of macrocyclic compounds with different guest molecules. Supramol Chem 2011. [DOI: 10.1080/10610278.2011.581281] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- J. B. Ghasemi
- a Chemistry Department, Faculty of Sciences , K. N. Toosi University of Technology , Tehran , Iran
| | - M. Salahinejad
- b Faculty of Chemistry , Tarbiat Moalem University , Tehran , Iran
| | - M. K. Rofouei
- b Faculty of Chemistry , Tarbiat Moalem University , Tehran , Iran
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11
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Katritzky AR, Kuanar M, Slavov S, Hall CD, Karelson M, Kahn I, Dobchev DA. Quantitative Correlation of Physical and Chemical Properties with Chemical Structure: Utility for Prediction. Chem Rev 2010; 110:5714-89. [DOI: 10.1021/cr900238d] [Citation(s) in RCA: 386] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Alan R. Katritzky
- Center for Heterocyclic Compounds, Department of Chemistry, University of Florida, Gainesville, Florida 32611
| | - Minati Kuanar
- Center for Heterocyclic Compounds, Department of Chemistry, University of Florida, Gainesville, Florida 32611
| | - Svetoslav Slavov
- Center for Heterocyclic Compounds, Department of Chemistry, University of Florida, Gainesville, Florida 32611
| | - C. Dennis Hall
- Center for Heterocyclic Compounds, Department of Chemistry, University of Florida, Gainesville, Florida 32611
| | - Mati Karelson
- Institute of Chemistry, Tallinn University of Technology, Akadeemia tee 15, Tallinn 19086, Estonia, and MolCode, Ltd., Soola 8, Tartu 51013, Estonia
| | - Iiris Kahn
- Institute of Chemistry, Tallinn University of Technology, Akadeemia tee 15, Tallinn 19086, Estonia, and MolCode, Ltd., Soola 8, Tartu 51013, Estonia
| | - Dimitar A. Dobchev
- Institute of Chemistry, Tallinn University of Technology, Akadeemia tee 15, Tallinn 19086, Estonia, and MolCode, Ltd., Soola 8, Tartu 51013, Estonia
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12
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Liu H, Wen Y, Luan F, Gao Y, Li X. Quantitative structure-λmax relationship study on flavones by heuristic method and radial basis function neural network. Anal Chim Acta 2009; 649:52-61. [DOI: 10.1016/j.aca.2009.07.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2009] [Revised: 06/27/2009] [Accepted: 07/03/2009] [Indexed: 11/30/2022]
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13
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Xu J, Xiong Q, Chen B, Wang L, Liu L, Xu W. Modeling the Relative Fluorescence Intensity Ratio of Eu(III) Complex in Different Solvents Based on QSPR Method. J Fluoresc 2008; 19:203-9. [DOI: 10.1007/s10895-008-0403-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2008] [Accepted: 07/14/2008] [Indexed: 10/21/2022]
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14
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Qi M, Zhou H, Ma X, Zhang B, Jefferies C, Yan B. Feasibility of a self-calibrated LC/MS/UV method to determine the absolute amount of compounds in their storage and screening lifecycle. JOURNAL OF COMBINATORIAL CHEMISTRY 2008; 10:162-5. [PMID: 18281955 DOI: 10.1021/cc800007k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Minghua Qi
- School of Pharmaceutical Sciences, Shandong University, Jinan, China
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15
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Chen HF. Quantitative predictions of gas chromatography retention indexes with support vector machines, radial basis neural networks and multiple linear regression. Anal Chim Acta 2008; 609:24-36. [DOI: 10.1016/j.aca.2008.01.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2007] [Revised: 09/17/2007] [Accepted: 01/02/2008] [Indexed: 11/25/2022]
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16
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Katritzky AR, Slavov SH, Dobchev DA, Karelson M. QSPR modeling of UV absorption intensities. J Comput Aided Mol Des 2007; 21:371-7. [PMID: 17563860 DOI: 10.1007/s10822-007-9118-y] [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: 11/14/2006] [Accepted: 04/23/2007] [Indexed: 10/23/2022]
Abstract
Literature UV absorption intensities at 260 nm and 25 degrees C in water of a diverse set of 805 organic compounds when analyzed by CODESSA Pro software using an initial pool of 800 + descriptors provide a significant QSPR correlation (R (2) = 0.692). Concurrently, a neural networks approach was used to develop a corresponding nonlinear model. The descriptors appearing in these models are discussed with respect to the physical nature of the UV absorption phenomenon.
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Affiliation(s)
- Alan R Katritzky
- Center for Heterocyclic Compounds, Department of Chemistry, University of Florida, Gainesville, FL 32611, USA.
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Chen Y, Monshouwer M, Fitch WL. Analytical Tools and Approaches for Metabolite Identification in Early Drug Discovery. Pharm Res 2006; 24:248-57. [PMID: 17048114 DOI: 10.1007/s11095-006-9162-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2006] [Accepted: 06/07/2006] [Indexed: 11/30/2022]
Abstract
Determination of the chemical structures of metabolites is a critical part of the early pharmaceutical discovery process. Understanding the structures of metabolites is useful both for optimizing the metabolic stability of a drug as well as rationalizing the drug safety profile. This review describes the current state of the art in this endeavor. The likely outcome of metabolism is first predicted by comparison to the literature. Then metabolites are synthesized in a variety of in vitro systems. The various approaches to LC/UV/MS are applied to learn information about these metabolites and structure hypotheses are made. Structures are confirmed by synthesis or NMR. The special topic of reactive metabolite structure determination is briefly addressed.
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Affiliation(s)
- Yuan Chen
- Drug Metabolism and Pharmacokinetics, Roche Palo Alto, 3431 Hillview Ave., Palo Alto, California 94304, USA
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Shi J, Luan F, Zhang H, Liu M, Guo Q, Hu Z, Fan B. QSPR Study of Fluorescence Wavelengths (λex/λem) Based on the Heuristic Method and Radial Basis Function Neural Networks. ACTA ACUST UNITED AC 2006. [DOI: 10.1002/qsar.200510142] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Mauser H, Roche O, Stahl M, Müller S. Prediction of UV and ESI−MS Signal Intensities. J Chem Inf Model 2005; 45:1039-46. [PMID: 16045299 DOI: 10.1021/ci0496548] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
All major pharmaceutical companies maintain large collections of compounds that are used either for screening against biological targets or as synthetic precursors. The quality assessment of these compounds is typically done by liquid chromatography combined with mass spectroscopy (LC/MS) and UV purity control. To facilitate the analysis of the analytical data, we have built computational models to predict UV and MS signal intensities under experimental LC/MS conditions. The discriminant partial-least-squares technique was used for classifying compounds into those most likely to yield a MS signal and others where the signal is below the detection limit (94% and 88% correct predictions, respectively). In the case of UV prediction, we compared this statistical linear-regression technique to a knowledge-based approach. A combination of both techniques proved to be the most reliable (96/98% correct predictions of UV-active/ UV-inactive compounds). Both models have been incorporated into the automated compound integrity profiling at F. Hoffmann-La Roche.
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Affiliation(s)
- Harald Mauser
- F. Hoffmann-La Roche Ltd., Pharmaceuticals Division, CH-4070 Basel, Switzerland.
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Feng D, Wang S, Zhuang Q, Guo P, Wu P, Han Z. Joint theoretical and experimental study of the UV absorption spectra of polybenzoxazoles. J Mol Struct 2004. [DOI: 10.1016/j.molstruc.2004.07.018] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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