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Int. J. Mol. Sci., Volume 7, Issue 11 (November 2006) – 6 articles , Pages 469-555

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601 KiB

Open AccessArticle

Design of Anti-HIV Ligands by Means of Minimal Topological Difference (MTD) Method

by Corina Duda-Seiman, Daniel Duda-Seiman, Dan Dragos, Mihai Medeleanu, Valentin Careja, Mihai V. Putz, Ana-Maria Lacrama, Adrian Chiriac, Remus Nutiu and Dan Ciubotariu

Int. J. Mol. Sci. 2006, 7(11), 537-555; https://doi.org/10.3390/i7110537 - 29 Nov 2006

Cited by 18 | Viewed by 10325

Abstract

Molecular modeling and MTD methods are useful tools to assess both qualitative(SAR) and quantitative (QSAR) chemical structure-biological activity relationships. The 1-[(2-hydroxiethoxi)-methyl]-6-(phenylthio)thymine congeners (HEPT ligands) show in vitroanti-viral activity against the type-1 human immunodeficiency virus (HIV-1), which is theetiologic agent of AIDS. This work shows an extensive QSAR study performed upon a largeseries of 79 HEPT ligands using the MTD and HyperChem molecular modeling methods.The studied HEPT ligands are HIV reverse-transcriptase inhibitors. Their geometries wereoptimized and conformational analysis was carried out to build the hypermolecule, whichallowed applying the MTD method. The hypermolecule was used for space mapping of thereceptor’s interaction site. The obtained results show that there are three 3D molecular zonesimportant for the anti-HIV biological activity of the HEPT ligands under study. Full article

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2395 KiB

Open AccessArticle

Binding of Fidarestat Stereoisomers with Aldose Reductase

by Dooil Kim, Suk-In Hong and Dae-Sil Lee

Int. J. Mol. Sci. 2006, 7(11), 519-536; https://doi.org/10.3390/i7110519 - 21 Nov 2006

Cited by 2 | Viewed by 7424

Abstract

The stereospecificity in binding to aldose reductase (ALR2) of two fidarestat {6-fluoro-2',5'-dioxospiro[chroman-4,4'-imidazolidine]-2-carboxamide} stereoisomers [(2S,4S)and (2R,4S)] has been investigated by means of molecular dynamics simulations using freeenergy integration techniques. The difference in the free energy of binding was found to be2.0 ± 1.7 kJ/mol in favour of the (2S,4S)-form, in agreement with the experimentalinhibition data. The relative mobilities of the fidarestats complexed with ALR2 indicate alarger entropic penalty for hydrophobic binding of (2R,4S)-fidarestat compared to (2S,4S)-fidarestat, partially explaining its lower binding affinity. The two stereoisomers differmainly in the orientation of the carbamoyl moiety with respect to the active site and rotationof the bond joining the carbamoyl substituent to the ring. The detailed structural andenergetic insights obtained from out simulations allow for a better understanding of thefactors determining stereospecific inhibitor-ALR2 binding in the EPF charges model. Full article

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415 KiB

Open AccessArticle

Expression of Myosin Light Chain Kinase in Kidney of Streptozotocin-Induced Diabetic Rats

by Huaqing Zhu, Xiaolin Zhang, Li Zuo, Qing Zhou, Shuyu Gui, Wei Wei and Yuan Wang

Int. J. Mol. Sci. 2006, 7(11), 510-518; https://doi.org/10.3390/i7110510 - 21 Nov 2006

Cited by 3 | Viewed by 8356

Abstract

Nephropathy is one of the most common complications of diabetes mellituswhich remains incompletely understood. We reported the expression of myosin light chainkinase (MLCK) in the kidney of diabetic rats and investigated the correlation betweenMLCK and diabetic nephropathy by observing the expression of MLCK. The diabetic modelrats were induced by an intraperitoneal injection of streptozotocin (STZ) and the insulin-treated rats were subcutaneously injected with protamine zine insulin 3u/d. The kidneyswere excised and immersed in 4% polyoxymethylene after 12 weeks later. The expression ofMLCK was analyzed by immunohistochemical staining and Western blot.Immunohistochemical analysis and Western blot assay indicated that the MLCK expressionwas higher in kidney of diabetic rats than that in control and it was decreased in kidney ofinsulin-treated rats. Our results suggested that the over expression of MLCK may be relatedwith the development of diabetic nephropathy. Full article

(This article belongs to the Special Issue Interaction of Biological Molecules)

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102 KiB

Open AccessReview

Application of Chromatographic and Electrophoretic Methods for the Analysis of Imidazolium and Pyridinium Cations as Used in Ionic Liquids

by P. Stepnowski

Int. J. Mol. Sci. 2006, 7(11), 497-509; https://doi.org/10.3390/i7110497 - 17 Nov 2006

Cited by 39 | Viewed by 9326

Abstract

Interest in ionic liquids for their potential in different chemical processes isconstantly increasing, as they are claimed to be environmentally benign – excellent, non-volatile solvents for a wide range of applications. The wide applicability of thesecompounds also demands reliable, relatively simple and reproducible analytical techniques.These methods must be applicable not only to different technical or natural matrices but alsoto the very low concentrations that are likely to be present in biological and environmentalsystems. In this review, therefore, methods for separating and analysing imidazolium- andpyridinium-type ionic liquids in aqueous matrices using high performance liquidchromatography (HPLC) and capillary electrophoresis (CE) are examined. The techniquesfor identifying ionic liquids are meant primarily to track the concentrations of ionic liquidsas residues not only in products and wastes but also in biological or environmental samples.The application of hyphenated techniques in this field is intended to selectively separate thequaternary entity from other cationic and non-ionic species present in the matrix, and toenable its fine-scale quantification. Nowadays, methods developed for cation analysis arebased mostly on reversed-phase high-performance liquid chromatography, ionchromatography, ion-pair chromatography and capillary electrophoresis, where variousbuffered mobile phases are used. Full article

(This article belongs to the Special Issue Ionic Liquids)

1104 KiB

Open AccessArticle

Triazoloquinazolines as Human A3 Adenosine Receptor Antagonists: A QSAR Study

by Dooil Kim, Suk-In Hong and Dae-Sil Lee

Int. J. Mol. Sci. 2006, 7(11), 485-496; https://doi.org/10.3390/i7110485 - 15 Nov 2006

Cited by 7 | Viewed by 17593

Abstract

Multiple linear regression analysis was performed on the quantitative structure-activity relationships (QSAR) of the triazoloquinazoline adenosine antagonists for human A3receptors. The data set used for the QSAR analysis encompassed the activities of 33triazoloquinazoline derivatives and 72 physicochemical descriptors. A template moleculewas derived using the known molecular structure for one of the compounds when bound tothe human A2B receptor, in which the amide bond was in a cis-conformation. All the testcompounds were aligned to the template molecule. In order to identify a reasonable QSARequation to describe the data set, we developed a multiple linear regression program thatexamined every possible combination of descriptors. The QSAR equation derived from thisanalysis indicates that the spatial and electronic effects is greater than that of hydrophobiceffects in binding of the antagonists to the human A3 receptor. It also predicts that a largesterimol length parameter is advantageous to activity, whereas large sterimol widthparameters and fractional positive partial surface areas are nonadvatageous. Full article

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169 KiB

Open AccessArticle

Full Analytic Progress Curves of Enzymic Reactions in Vitro

by Mihai V. Putz, Ana-Maria Lacrama and Vasile Ostafe

Int. J. Mol. Sci. 2006, 7(11), 469-484; https://doi.org/10.3390/i7110469 - 2 Nov 2006

Cited by 27 | Viewed by 12171

Abstract

Assuming the in vitro conditions for the enzyme-catalyzed reactions, the basic Michaelis-Menten description is modified in a logistic (mathematical) manner such that the inherent limitations that appear in the previous method are removed. Beside its generality, the reliability of the present approach is [...] Read more.

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