rDock: A Fast, Versatile and Open Source Program for Docking Ligands to Proteins and Nucleic Acids

Identification of chemical compounds with specific biological activities is an important step in both chemical biology and drug discovery. When the structure of the intended target is available, one approach is to use molecular docking programs to assess the chemical complementarity of small molecules with the target; such calculations provide a qualitative measure of affinity that can be used in virtual screening (VS) to rank order a list of compounds according to their potential to be active. rDock is a molecular docking program developed at Vernalis for high-throughput VS (HTVS) applications. Evolved from RiboDock, the program can be used against proteins and nucleic acids, is designed to be computationally very efficient and allows the user to incorporate additional constraints and information as a bias to guide docking. This article provides an overview of the program structure and features and compares rDock to two reference programs, AutoDock Vina (open source) and Schrodinger's Glide (commercial). In terms of computational speed for VS, rDock is faster than Vina and comparable to Glide. For binding mode prediction, rDock and Vina are superior to Glide. The VS performance of rDock is significantly better than Vina, but inferior to Glide for most systems unless pharmacophore constraints are used; in that case rDock and Glide are of equal performance. The program is released under the Lesser General Public License and is freely available for download, together with the manuals, example files and the complete test sets, at http://rdock.sourceforge.net/

EDTA: the chelating agent under environmental scrutiny

The chelating agent EDTA (ethylenediaminetetraacetic acid) is a compound of massive use world wide with household and industrial applications, being one of the anthropogenic compounds with highest concentrations in inland European waters. In this review, the applications of EDTA and its behavior once it has been released into the environment are described. At a laboratory scale, degradation of EDTA has been achieved; however, in natural environments studies detect poor biodegradability. It is concluded that EDTA behaves as a persistent substance in the environment and that its contribution to heavy metals bioavailability and remobilization processes in the environment is a major concern.

Chelating Adsorbents in Purification of Hydrometallurgical Solutions

In this thesis, equilibrium and dynamic sorption properties of weakly basic chelating adsorbents were studied to explain removal of copper, nickel from a concentrated zinc sulfate solution in a hydrometallurgical process. Silica-supported chelating composites containing either branched poly(ethyleneimine) (BPEI) or 2-(aminomethyl)pyridine (AMP) as a functional group were used. The adsorbents are commercially available from Purity Systems Inc, USA as WP-1® and CuWRAM®, respectively. The fundamental interactions between the adsorbents, sulfuric acid and metal sulfates were studied in detail and the results were used to find the best conditions for removal of copper and nickel from an authentic ZnSO4 process solution. In particular, the effect of acid concentration and temperature on the separation efficiency was considered. Both experimental and modeling aspectswere covered in all cases. Metal sorption is considerably affected by the chemical properties of the studied adsorbents and by the separation conditions. In the case of WP-1, acid affinity is so high that column separation of copper, nickel and zinc has to be done using the adsorbent in base-form. On the other hand, the basicity of CuWRAM is significantly lower and protonated adsorbent can be used. Increasing temperature decreases the basicity and the metals affinity of both adsorbents, but the uptake capacities remain practically unchanged. Moreover, increasing temperature substantially enhances intra-particle mass transport and decreases viscosities thus allowing significantly higher feed flow rates in the fixed-bed separation. The copper selectivity of both adsorbents is very high even in the presence of a 250-fold excess of zinc. However, because of the basicity of WP-1, metal precipitation is a serious problem and therefore only CuWRAM is suitable for the practical industrial application. The optimum temperature for copper removal appears to be around 60 oC and an alternative solution purification method is proposed. The Ni/Zn selectivity of both WP-1 and CuWRAM is insufficient for removal of the very small amounts of nickel present in the concentrated ZnSO4 solution.

Synthesis, structure and physicochemical properties of zinc and copper complexes based on sulfonamides containing 8-aminoquinoline ligands

Sulfonamides obtained by reaction of 8-aminoquinoline with 4-nitrobenzenesulfonylchloride and 2,4,6-triisopropylbenzenesulfonyl chloride were used to synthesize coordination compounds with CuII and ZnII with a ML2 composition. Determination of the crystal structures of the resulting zinc and copper complexes by X-ray diffraction show a distorted tetrahedral environment for the [Cu(qnbsa)2], [Cu(qibsa)2] and [Zn(qibsa)2] complexes in which the sulfonamide group acts as a bidentate ligand through the nitrogen atoms from the sulfonamidate and quinoline groups. The complex [Zn(qnbsa)2] crystallizes with a water molecule from the solvent and the Zn is five-coordinated and shows a bipyramidal-trigonal geometry. The electrochemical and electronic spectroscopy properties of the copper complexes are also discussed.

Magnetic, thermal and spectral properties of Ni(II) 2,3- , 3,5- and 2,6-dimethoxybenzoates

Complexes of Ni(II) 2,3-, 3,5- and 2,6-dimethoxybenzoates have been synthesized, their physico-chemical properties have been compared and the influence of the position of -OCH3 substituent on their properties investigated. The analysed compounds are crystalline, hydrated salts with green colour. The carboxylate ions show a bidentate chelating or bridging coordination modes. The thermal stabilities of Ni(II) dimethoxybenzoates were investigated in air in the range of 293-1173 K. The complexes decompose in three steps, yelding the NiO as the final product of decomposition. Their solubilities in water at 293 K are in the order of 10-2-10-4 mol×dm-3. The magnetic susceptibilities for the analysed dimethoxybenzoates of Ni(II) were measured over the range of 76-303 K and the magnetic moments were calculated. The results reveal that the complexes are the high-spin ones and the ligands form the weak electrostatic field in the octahedral coordination sphere of the central Ni(II) ion. The various position -OCH3 groups in benzene ring cause the different steric, mesomeric and inductive effects on the electron density in benzene ring.

Complexes of 3,4-dimethoxybenzoic acid anion with Cu(II), Co(II), La(III), and Nd(III)

Physico-chemical properties of 3,4-dimethoxybenzoates of Co(II), Cu(II), La(III) and Nd(III) were studied. The complexes were obtained as hydrated or anhydrous polycrystalline solids with a metal ion-ligand mole ratio of 1 : 2 for divalent ions and of 1 : 3 in the case of trivalent cations. Their colours depend on the kind of central ion: pink for Co(II) complex, blue for Cu(II), white for La(III) and violet for Nd(III) complexes. The carboxylate groups in these compounds are monodentate, bidentate bridging or chelating and tridentate ligands. Their thermal decomposition was studied in the range of 293-1173 K. Hydrated complexes lose crystallization water molecules in one step and form anhydrous compounds, that next decompose to the oxides of respective metals. 3,4 - Dimethoxybenzoates of Co(II) is directly decomposed to the appropriate oxide and that of Nd(III) is also ultimately decomposed to its oxide but with the intemediate formation of Nd2O2CO3.. The magnetic moment values of 3,4-dimethoxybenzoates determined in the range of 76-303 K change from 4.22 µB to 4.61 µB for Co(II) complex , from 0.49 µB to 1.17 µB for Cu(II) complex , and from 2.69 µB to 3.15 µB for Nd(III) complex.

Comparison of some properties of 2,3 - and 3,4 - dimethoxybenzoates of Cu(II), Co(II) and Nd(III)

The physicochemical properties of 2,4-, and 3,4- dimethoxybenzoates of Cu(II), Co(II) and Nd(III) were studied and compared to observe the -OCH3 substituent positions in benzene ring on the character of complexes. The analysed compounds are crystalline hydrated or anhydrous salts with colours depending on the kind of central ions: blue for Cu(II), pink for Co(II) and violet for Nd(III) complexes. The carboxylate groups bind as monodentate, bidentate bridging or chelating and even tridentate ligands. Their thermal stabilities were studied in air at 293-1173K. When heated the hydrated complexes release the water molecules and form anhydrous compounds which are then decomposed to the oxides of respective metals. Their magnetic moment values were determined in the range of 76-303K. The results reveal the compounds of Nd(III) and Co(II) to be the high-spin and that of Cu(II) forms dimer. The various positions of -OCH3 groups in benzene ring influence some of physicochemical properties of analysed compounds.

Biheterocyclic ligands: synthesis, characterization and coordinating properties of bis(4-amino-5-mercapto-1,2,4-triazol-3-yl) alkanes with transition metal ions and their thermokinetic and biological studies

The Co(II), Ni(II) and Cu(II) metal ions complexes of Bis(4-amino-5-mercapto-1,2,4-triazol-3-yl) alkanes (BATs) have been prepared and characterized by elemental analysis, conductivity measurements infrared, magnetic susceptibility, the electronic spectral data and thermal studies. Based on spectral and magnetic results, the ligands are tetradentate coordinating through the N and S-atoms of BATs; six-coordinated octahedral or distorted octahedral and some times four-coordinated square planar were proposed for these complexes. Activation energies computed for the thermal decomposition steps were compared. The ligands and their metal complexes were tested in vitro for their biological effects. Their activities against two gram-positive, two gram-negative bacteria and two fungal species were found to vary from moderate to very strong.

Complexes of 4-chlorophenoxyacetates of Nd(III), Gd(III) and Ho(III)

The complexes of 4-chlorophenoxyacetates of Nd(III), Gd(III) and Ho(III) have been synthesized as polycrystalline hydrated solids, and characterized by elemental analysis, spectroscopy, magnetic studies and also by X-ray diffraction and thermogravimetric measurements. The analysed complexes have the following colours: violet for Nd(III), white for Gd(III) and cream for Ho(III) compounds. The carboxylate groups bind as bidentate chelating (Ho) or bridging ligands (Nd, Gd). On heating to 1173K in air the complexes decompose in several steps. At first, they dehydrate in one step to form anhydrous salts, that next decompose to the oxides of respective metals. The gaseous products of their thermal decomposition in nitrogen were also determined and the magnetic susceptibilites were measured over the temperature range of 76-303K and the magnetic moments were calculated. The results show that 4-chlorophenoxyacetates of Nd(III), Gd(III) and Ho(III) are high-spin complexes with weak ligand fields. The solubility value in water at 293K for analysed 4-chlorophenoxyacetates is in the order of 10-4mol/dm³.

Metallien eluointi kelatoivasta ioninvaihtimesta

Kelatoivat ioninvaihtimet ovat yleensä makrohuokoisia hartseja, joiden avulla metalleja poistetaan ja otetaan mahdollisesti talteen teollisuuden puhdistettavista jätevirroista. Ne muodostavat metalli-ionien kanssa komplekseja runkomateriaaliin kovalenttisesti liitettyjen aktiivisten funktionaalisten ryhmiensä välityksellä. Ioninvaihtimen selektiivisyys eri metalli-ioneja kohtaan vaihtelee riippuen siihen liitetystä kelatoivasta ryhmästä. Työssä tutkitaan metallien tarttumista kelatoiviin ioninvaihtimiin, sekä niiden eluoitumista adsorbentistaan. Kelatoivat ioninvaihtimet sitovat metalli-ioneja tehokkaasti ligandiensa monihampaisuudesta johtuen. Metallien tarttuminen kelatoivaan ioninvaihtimeen ei kuitenkaan ole yksiselitteistä, vaan siihen vaikuttaa muun muassa pH yhdessä monen muun tekijän kanssa. Ioninvaihtimien selektiivisyyttä tarkastellaan työssä lähinnä kovien ja pehmeiden happojen ja emästen HSAB -teorian näkökulmasta. Regeneroinnilla ioninvaihdin saadaan jälleen alkuperäiseen muotoonsa, minkä jälkeen se voidaan käyttää uudelleen. Yleensä regenerointi suoritetaan kemiallisesti. Tässä työssä ioninvaihtimien regenerointia ja kohdemetallin eluointia tarkastellaan paitsi teoriassa, myös kokeellisessa osuudessa. Kokeellisessa osuudessa tutkitaan kuparin (Cu2+) eluoitumista kelatoivasta Dowex M-4195 kationinvaihtohartsista. Kokeissa hartsi ladattiin kuparilla erillisessä panoksessa kuparin ollessa syöttöliuoksessa kuparisulfaattina. Eluointiliuoksina käytettiin 2 ja 5 molaarista rikkihappoa, sekä 2 molaarista ammoniumhydroksidia. Eluointi suoritettiin panostoimisena kolonniajona ja eluaatista otetut näytteet analysoitiin atomiadsorptiospektrofotometrillä. Analyysitulokset esitetään läpäisykäyrinä, joiden perusteella 2M ammoniumhydroksidi on kolmesta tutkitusta eluentista tehokkain eluoimaan kuparia Dowex M-4195 hartsista.

Fluorescent ligands for studying neuropeptide receptors by confocal microscopy

This paper reviews the use of confocal microscopy as it pertains to the identification of G-protein coupled receptors and the study of their dynamic properties in cell cultures and in mammalian brain following their tagging with specific fluorescent ligands. Principles that should guide the choice of suitable ligands and fluorophores are discussed. Examples are provided from the work carried out in the authors' laboratory using custom synthetized fluoresceinylated or BODIPY-tagged bioactive peptides. The results show that confocal microscopic detection of specifically bound fluorescent ligands permits high resolution appraisal of neuropeptide receptor distribution both in cell culture and in brain sections. Within the framework of time course experiments, it also allows for a dynamic assessment of the internalization and subsequent intracellular trafficking of bound fluorescent molecules. Thus, it was found that neurotensin, somatostatin and mu- and delta-selective opioid peptides are internalized in a receptor-dependent fashion and according to receptor-specific patterns into their target cells. In the case of neurotensin, this internalization process was found to be clathrin-mediated, to proceed through classical endosomal pathways and, in neurons, to result in a mobilization of newly formed endosomes from neural processes to nerve cell bodies and from the periphery of cell bodies towards the perinuclear zone. These mechanisms are likely to play an important role for ligand inactivation, receptor regulation and perhaps also transmembrane signaling.

Disintegrins: integrin selective ligands which activate integrin-coupled signaling and modulate leukocyte functions

Extracellular matrix proteins and cell adhesion receptors (integrins) play essential roles in the regulation of cell adhesion and migration. Interactions of integrins with the extracellular matrix proteins lead to phosphorylation of several intracellular proteins such as focal adhesion kinase, activating different signaling pathways responsible for the regulation of a variety of cell functions, including cytoskeleton mobilization. Once leukocytes are guided to sites of infection, inflammation, or antigen presentation, integrins can participate in the initiation, maintenance, or termination of the immune and inflammatory responses. The modulation of neutrophil activation through integrin-mediated pathways is important in the homeostatic control of the resolution of inflammatory states. In addition, during recirculation, T lymphocyte movement through distinct microenvironments is mediated by integrins, which are critical for cell cycle, differentiation and gene expression. Disintegrins are a family of low-molecular weight, cysteine-rich peptides first identified in snake venom, usually containing an RGD (Arg-Gly-Asp) motif, which confers the ability to selectively bind to integrins, inhibiting integrin-related functions in different cell systems. In this review we show that, depending on the cell type and the microenvironment, disintegrins are able to antagonize the effects of integrins or to act agonistically by activating integrin-mediated signaling. Disintegrins have proven useful as tools to improve the understanding of the molecular events regulated by integrin signaling in leukocytes and prototypes in order to design therapies able to interfere with integrin-mediated effects.

The study of ligand binding specificities of the lipid binding proteins : recombinant human a-tocopherol transport protein (a-ttp), supernatant protein factor (spf) and S. cerevisiae Sec 14p for vitamin e (rrr-a-tocopherol) and other hydrophobic ligands.

One of the various functions of proteins in biological systems is the transport of small molecules, for this purpose proteins have naturally evolved special mechanisms to allow both ligand binding and its subsequent release to a target site; a process fundamental to many biological processes. Transport of Vitamin E (a-tocopherol), a lipid soluble antioxidant, to membranes helps in the protection of polyunsaturated fatty acids against peroxidative damage. In this research, the ligand binding characteristics of several members of the CRALTRIO family of lipid binding proteins was examined; the recombinant human a-Tocopherol Transfer Protein (a-TIP), Supernatant Protein Factor (SPF)ffocopherol Associated Protein (TAP), Cellular Retinaldehyde Binding Protein (CRALBP) and the phosphatidylinositol transfer protein from S. cerevisiae Sec 14p. Recombinant Sec 14p was expressed and purified from E. coli for comparison of tocopherol binding to the two other recombinant proteins postulated to traffic a-tocopherol. Competitive binding assays using [3H]-a-tocopherol and Lipidex-l000 resin allowed determination of the dissociation constants ~) of the CRAL-TRIO proteins for a-tocopherol and - 20 hydrophobic ligands for evaluation of the possible biological relevance of the binding interactions observed. The KIs (nM) for RRR-a-tocopherol are: a-TIP: 25.0, Sec 14p: 373, CRALBP: 528 and SPFffAP: 615. This indicates that all proteins recognize tocopherol but not with the same affinity. Sec 14p bound its native ligand PI with a KI of381 whereas SPFffAP bound PI (216) and y-tocopherol (268) similarly in contrast to the preferential binding ofRRR-a-tocopherol by a-TIP. Efforts to adequately represent biologically active SPFff AP involved investigation of tocopherol binding for several different recombinant proteins derived from different constructs and in the presence of different potential modulators (Ca+2, Mg+2, GTP and GDP); none of these conditions enhanced or inhibited a-tocopherol binding to SPF. This work suggests that only aTTP serves as the physiological mediator of a-tocopherol, yet structural homology between proteins allows common recognition of similar ligand features. In addition, several photo-affmity analogs of a-tocopherol were evaluated for their potential utility in further elucidation of a-TTP function or identification of novel tocopherol binding proteins.

Design and synthesis of new monoterpenoid derived ligands for asymmetric catalysis /

The work to be presented herein illustrates several important facts. First, the synthesis of BIBOL (19), a 1,4-diol derived from the monoterpene camphor has allowed us to demonstrate that oxidative dimerizations of enolates can, and do proceed with nearly complete diastereoselectivity under kinetically controlled conditions. The yield of BIBOL is now 50% on average, with a 10% yield of a second diastereomer, which is likely the result of a non-kinetic hydride reduction, thereby affording the epimeric alcohol, 20, coupled on the exo face of camphor. This implies the production of 60% of a single coupling diastereomer. No other diastereomers from the reduction were observed. The utility of BEBOL has been illustrated in early asymmetric additions of diethylzinc to aryl aldehydes, with e.e.'s as high as 25-30%. '^' To further the oxidative coupling work, the same methodology which gave rise to BIBOL was applied to the chiral pool ketone, menthone. Interestingly, this gave an excellent yield of the a-halohydrin (31), which is the result of a chlorination of menthone. This result clearly indicates the high stereoselectivity of the process regardless of the outcome, and has illustrated an interesting dichotomy between camphor and menthone. The utility of the chlorination product as a precursor other chiral ligands is currently being investigated. > ' Finally, a new series of 1,3-diols as well as a new aminoalcohol have successfully been synthesized from highly diastereoselective aldol/mannich reactions. Early studies have indicated their potential in asymmetric catalysis, while employing pi-stack interactions as a means of controlling enantioselective aldol reactions.

Synthesis of fluorescent analogues of a-tocopherol as ligands for the human a-tocopherol transfer protein (a-TTP) /

To further understand in vivo localization and trafficking of a-tocopherol (a-Toe), the most biologically active form of vitamin E, between lipid environments, tocopherols are required that can be followed by teclu1iques such as confocal microscopy and fluorescence resonance energy transfer (FRET) assays. To this end, sixteen fluorescent analogues of a-tocopherol (la-d [(1)anthroy loxy -a-tocopherols, A O-a-Toes], 2a-d [w-nitro benzoxadiazole-a-tocopherols, NBD-aToes], 3a-d [w-dansyl-a-tocopherols, DAN-a-Toes], and 4a-d [w-N-methylanthranilamide-atocopherols, NMA-a-TocsD were prepared by substituting fluorescent labels at the terminus of w-functionalized alkyl chains extending from C-2 of the chroman ring while retaining key binding features of the natural ligand. These compounds were prepared starting from (S)-Trolox® acid VIa esterification, protection, and reduction producing the silyl-protected (S)-Trolox aldehyde that was coupled using Wittig chemistry to different w-hydroxyalkylphosphonium bromides. Reduction of the alkene generated the w-hydroxy functionalized 2-n-alkyl intermediates 9a-d having the necessary 2R stereochemistry. A series of functional group manipulations including mesylation, substitution with azide, and hydride reduction provided w-amino functionalized intermediates 12a-d as well. Coupling intermediates 9a-d and 12a-d with the selected fluorophores (9- anthracene carboxylic acid, 4-chloro-7-nitrobenz-2-oxa-l,3-diazole, 5- dimethylaminonapthalene-l-sulfonyl chloride, and I-methyl-2H-3,1-benzoxazine-2,4(1H)dione), followed by deprotection of the phenolic silyl group, gave the desired fluorescent ligands la-d, 2a-d, 3a-d and 4a-d in good yield. Assessment of their binding affinities with recombinant human a-tocopherol transfer protein (ha-TTP) utilizing fluorescent titration binding assays identified competent ligands for further use in protein studies. Compounds Id (C9-AO-a-Toc) and 2d (C9-NBD-a-Toc) both having nonyl alkyl chain extensions between the chromanol and fluorophore were shown to bind specifically to ha-TTP with dissociation constants (KdS) of approximately 280 nM and 55 nM respectively, as compared to 25 nM for the natural ligand 2R,4'R,^'R-a-tocophQxoL.