AstexViewer: a visualisation aid for structure-based drug design

AstexViewer is a Java molecular graphics program that can be used for visualisation in many aspects of structure-based drug design. This paper describes its functionality, implementation and examples of its use. The program can run as an Applet in a web browser allowing structures to be displayed without installing additional software. Applications of its use are described for visualisation and as part of a structure based design platform. The software is being made freely available to the community and may be downloaded from http://www.astex-technology.com/AstexViewer.     

1,1′-Biisoquinolines—Neglected Ligands in the Heterocyclic Diimine Family That Provoke Stereochemical Reflections

1,1′-Biisoquinolines are a class of bidentate nitrogen donor ligands in the heterocyclic diimine family. This review briefly discusses their properties and the key synthetic pathways available and then concentrates upon their coordination behaviour. The ligands are of interest as they exhibit the phenomenon of atropisomerism (hindered rotation about the C1–C1′ bond). A notation for depicting the stereochemistry in coordination compounds containing multiple stereogenic centers is developed. The consequences of the chirality within the ligand on the coordination behaviour is discussed in detail.     

Protein-ligand docking against non-native protein conformers

In the validation of protein-ligand docking protocols, performance is mostly measured against native protein conformers, i.e. each ligand is docked into the protein conformation from the structure that contained that ligand. In real-life applications, however, ligands are docked against non-native conformations of the protein, i.e. the apo structure or a structure of a different protein-ligand complex. Here, we have constructed an extensive test set for assessing docking performance against non-native protein conformations. This new test set is built on the Astex Diverse Set (which we recently constructed for assessing native docking performance) and contains 1112 non-native structures for 65 drug targets. Using the protein-ligand docking program GOLD, the Astex Diverse Set and the new Astex Non-native Set, we established that, whereas docking performance (top-ranked solution within 2 A rmsd of the experimental binding mode) is approximately 80% for native docking, this drops to 61% for non-native docking. A similar drop-off is observed for sampling performance (any solution within 2 A): 91% for native docking vs 72% for non-native docking. No significant differences were observed between docking performance against apo and nonapo structures. We found that, whereas small variations in protein conformation are generally tolerated by our rigid docking protocol, larger protein movements result in a catastrophic drop-off in performance. Some docking performance and nearly all sampling performance can be recovered by considering dockings produced against a small number of non-native structures simultaneously. Docking against non-native structures of complexes containing ligands that are similar to the docked ligand also significantly improves both docking performance and sampling performance.     

Bioconcentration of zinc and its effect on the biochemical constituents of the gill tissues of Labeo rohita: An FT-IR study

In the present work, an attempt has been made to assess the bioconcentration and distribution of zinc on the selected organs of Labeo rohita and to study the effect of zinc exposure on the biochemical constitutions of gill tissues of L. rohita by using FT-IR Spectroscopy. The concentration pattern in the organs reveals that the liver is the prime site of metal binding and muscle accumulates least metal concentration. The accumulation profile is in the order: liver > gill > kidney > brain > bone > muscle. It has also been observed that the administration of chelating agent d-Penicillamine (DPA) reduces the zinc concentration in all tissues more effectively than the administration of the chelating agent Ethylene Diamine Tetra Acetic acid. The FT-IR spectra reveal that zinc exposure causes significant changes in the biochemical constitutions of the gill tissues. It causes an alteration in the protein secondary structures by decreasing the α-helix and increasing the β-sheet contents. Further, it has been observed that the administration of chelating agent DPA improves the protein and lipid contents in the gill tissues compared to zinc exposed tissues. This result shows that DPA is the effective chelator of zinc in reducing the body burden of L. rohita fingerlings. In conclusion, the findings of the current study suggest that zinc exposure causes significant changes in both lipids and proteins of the gill tissues, and changes the protein profile in favour of β-sheet structure.     

Arsenic-Induced Biochemical Changes in Labeo rohita Kidney: An FTIR Study

ABSTRACT

Arsenic is a toxic heavy metal that occurs naturally in water, soil, and air. It is widespread in the environment as a consequence of both anthropogenic and natural processes. In the current study, an attempt has been made to analyze the arsenic-induced molecular changes in macromolecular components like proteins and lipids in the kidney tissues of edible fish Labeo rohita using Fourier transform infrared (FTIR) spectroscopy. The FTIR spectrum of kidney tissue is quite complex and contains several bands arising from the contribution of different functional groups. The detailed spectral analyses were performed in three distinct wave number regions, namely 3600–3050 cm^?1, 3050–2800 cm^?1, and 1800–800 cm^?1. The current study shows that the kidney tissues are more vulnerable to arsenic intoxication. FTIR spectra reveal significant differences in both absorbance intensities and areas between control and arsenic-intoxicated kidney tissues; this result indicates that arsenic intoxication induces significant alteration on the major biochemical constituents such as lipids and proteins and leads to compositional and structural changes in kidney tissues at the molecular level. The current study confirms that FTIR spectroscopy can be successfully applied to toxicologic and biological studies.     

Vibrational spectroscopy of structural defects in oligothiophenes

Vibrational spectra of oligothiophenes with structural defects are calculated within the density-functional-theory methodology. The effects of the defective αβ linkages on the infrared (IR) and Raman spectra are characterized from calculations of all isomers up to the hexamer. The signatures of αβ linked monomers can be found in IR spectra from broken symmetry arguments which result in absorptions localized in the defective region. The positions of the absorption peaks in the Raman spectra seem to be unaffected by the presence of such defects; however, strong reductions in the intensities are observed because of the shortening of the conjugation length.     

Preparation and photochemistry of cobalt(III) amino and amino acidato complexes containing tripodal polypyridine ligands

The photochemical reactivities of cobalt(III)-diamine and cobalt(III)-amino acid compounds have been compared using complexes that also contain polypyridyl ligands. Metallacyclic complexes result from UV-induced photodecarboxylation reactions of the amino acid complexes. UV-irradiation of closely related complexes with amine donors replacing the carboxylate donors does not lead to the production of the same metallacyclic products. The reported UV-induced fragmentation of amine donors and subsequent metallacycle formation appears not to be a general reaction. Nine cobalt(III) complexes of polypyridyl ligands have been structurally characterised, including four that also contain amino acid ligands and one that contains a three-membered metallacyclic ring.     

Sensitivity of molecular docking to induced fit effects in influenza virus neuraminidase

Many proteins undergo small side chain or even backbone movements on binding of different ligands into the same protein structure. This is known as induced fit and is potentially problematic for virtual screening of databases against protein targets. In this report we investigate the limits of the rigid protein approximation used by the docking program, GOLD, through cross-docking using protein structures of influenza neuraminidase. Neuraminidase is known to exhibit small but significant induced fit effects on ligand binding. Some neuraminidase crystal structures caused concern due to the bound ligand conformation and GOLD performed poorly on these complexes. A `clean' set, which contained unique, unambiguous complexes, was defined. For this set, the lowest energy structure was correctly docked (i.e. RMSD < 1.5 Å away from the crystal reference structure) in 84% of proteins, and the most promiscuous protein (1mwe) was able to dock all 15 ligands accurately including those that normally required an induced fit movement. This is considerably better than the 70% success rate seen with GOLD against general validation sets. Inclusion of specific water molecules involved in water-mediated hydrogen bonds did not significantly improve the docking performance for ligands that formed water-mediated contacts but it did prevent docking of ligands that displaced these waters. Our data supports the use of a single protein structure for virtual screening with GOLD in some applications involving induced fit effects, although care must be taken to identify the protein structure that performs best against a wide variety of ligands. The performance of GOLD was significantly better than the GOLD implementation of ChemScore and the reasons for this are discussed. Overall, GOLD has shown itself to be an extremely good, robust docking program for this system.     

The effect of arsenic exposure on the biochemical and mineral contents of Labeo rohita bones: An FT-IR study

Arsenic compounds are ubiquitous and widespread in the environment as a result of natural or anthropogenic occurrence. Fish are the major source of protein for human consumption. They are also a source of contamination, because of the amounts of heavy elements they can contain, some of which are highly toxic. Fish bones are high in calcium, which is an essential mineral for normal body function. It consists of water, organic material, and mineral matter. Chelating agents have been used clinically as antidotes for acute and chronic metal intoxications. In the present study, an attempt is made to investigate the bio-accumulation of arsenic and its effect on the biochemical and mineral contents of Labeo rohita bones using, Fourier transform infrared (FT-IR) spectroscopy. The results of the present study indicate that arsenic exposure induces significant reduction on the biochemical and mineral contents of the L. rohita bones. Further, the DMSA treatment significantly improves these levels. This shows that DMSA is an effective chelator for arsenic toxicity. Quantitative curve-fitting analyses of amide I band have proved useful in studying the nature and the extent of protein conformational changes. A decrease in α-helical and random coil structures and an increase in β-sheet structures have been observed due to arsenic exposure. In conclusion, the present study shows that the FT-IR spectroscopy coupled with second derivative and curve-fitting analysis gives useful information about the biochemical and mineral contents of the L. rohita bones.