MetLigDB: a web-based database for the identification of chemical groups to design metalloprotein inhibitors

2011 ◽  
Vol 44 (4) ◽  
pp. 878-881 ◽  
Author(s):  
Hwanho Choi ◽  
Hongsuk Kang ◽  
Hwangseo Park
Keyword(s):  
Drug Discovery ◽  
Metal Ions ◽  
Metal Ion ◽  
Central Metal ◽  
Amino Acid Residues ◽  
Web Based ◽  
Additional Information ◽  
Chemical Groups ◽  
Insight Into ◽  
Chelating Groups

MetLigDB (http://silver.sejong.ac.kr/MetLigDB) is a publicly accessible web-based database through which the interactions between a variety of chelating groups and various central metal ions in the active site of metalloproteins can be explored in detail. Additional information can also be retrieved, including protein and inhibitor names, the amino acid residues coordinated to the central metal ion, and the binding affinity of the inhibitor for the target metalloprotein. Although many metalloproteins have been considered promising targets for drug discovery, it is difficult to discover new inhibitors because of the difficulty in designing a suitable chelating moiety to impair the catalytic activity of the central metal ion. Because both common and specific chelating groups can be identified for varying metal ions and the associated coordination environments, MetLigDB is expected to give users insight into designing new inhibitors of metalloproteins for drug discovery.

Solvent clustering, polar network density, and thermodynamic interactions in coordination polymers: an inverse gas chromatography study of metal-ion-containing polyesters of poly(diethylene glycol-co-succinic acid)

1995 ◽  
Vol 73 (11) ◽  
pp. 1855-1861 ◽  
Author(s):  
G. Julius Vancso ◽  
Zhanjie Tan
Keyword(s):  
Gas Chromatography ◽  
Metal Ions ◽  
Succinic Acid ◽  
Diethylene Glycol ◽  
Metal Ion ◽  
Inverse Gas Chromatography ◽  
Volume Fraction ◽  
Central Metal ◽  
Cluster Integrals ◽  
Finite Concentration

The spatial distribution of toluene and THF in the polyester poly(diethylene glycol-co-succinic acid) and its Mg2+-containing "telechelic" derivative was described by Kirkwood–Buff–Zimm (KBZ) cluster integrals. The values of KBZ integrals as a function of the volume fraction of solvent in the polymer–solvent systems were obtained from finite concentration inverse gas chromatography measurements utilizing the elution-on-a-plateau technique. The results show that toluene has a higher self-affinity to form clusters in the pure polyester than THF, which is more homogeneously distributed in the polymer. Data for preferential solvation indicate that a segregation of parts of the polymer chains is present in the toluene–polyester system. When metal ions are introduced, the self-affinity of the solvent molecules to gather increases, whereas solvent clusters of toluene form in the free volume, and the gathering of the THF is likely to take place close to the metal ions. Based on the electron donacity values of the various donor groups present in the metal-ion-containing polymer it was assumed that THF in the Mg2+-containing polyester will be bound to the central metal ion while the apolar toluene will participate in the solvation of the apolar parts of the polymer and will be "repelled" from the ion-containing regions. The concentration of these ionic centres, which act as effective cross-links in the coordination polymer, was determined from measurements of thermodynamic activity. A comparison of the experimental and estimated effective cross-link density values indicates a nearly atomic dispersion of Mg2+ in the metal-ion-containing polyesters. Keywords: inverse gas chromatography, cluster integrals, solvent partition in polymers, metal-ion-containing polyesters, Flory–Huggins interaction parameter.

scholarly journals Synthesis and photovoltaic properties of octacarboxy-metallophthalocyanine dyes applied in dye-sensitized solar cells

2012 ◽  
Vol 77 (9) ◽  
pp. 1223-1237 ◽  
Author(s):  
Ling Jin ◽  
Wei Chen ◽  
Dajun Chen
Keyword(s):  
Solar Cells ◽  
Metal Ions ◽  
Metal Ion ◽  
Dye Sensitized Solar Cells ◽  
Closed Shell ◽  
Open Shell ◽  
Central Metal ◽  
Photovoltaic Properties ◽  
Dye Sensitized ◽  
Sensitized Solar Cells

A series of octacarboxy-metallophthalocyanine dyes, i.e., MgOCPc, MnOCPc, FeOCPc and ZnOCPc with different central metal ions were designed and synthesized by microwave irradiation. The effects of the introduction of different metal ions with variant 3d orbitals (3d0, 3d5, 3d6, and 3d10, respectively) in the centre of the phthalocyanine rings on the thermal, photophysical, and electrochemical properties of octacarboxy-metallophthalocyanines were characterized and evaluated in details. The results showed that ZnOCPc and MgOCPc with closed-shell metal ions and FeOCPc with an open-shell metal ion had excellent thermal property. However, MnOCPc with a half-full-shell metal ion had a lowest decomposition temperature and largest Q band red shifts. By theoretical calculation, the energy gaps of MgOCPc, MnOCPc, FeOCPc and ZnOCPc were 0.11, 0.10, 0.20 and 0.22V, respectively. Applied in TiO2 nanocrystalline dye-sensitized solar cells (DSSC), the photovoltaic properties of the four dyes were obtained under AM1.5 irradiation (100 mW cm-2).

Influence of crystal structure, ligand environment and morphology on CoL-edge XAS spectral characteristics in cobalt compounds

2015 ◽  
Vol 22 (6) ◽  
pp. 1450-1458 ◽  
Author(s):  
D. K. Bora ◽  
X. Cheng ◽  
M. Kapilashrami ◽  
P. A. Glans ◽  
Y. Luo ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Electronic Structure ◽  
Metal Ion ◽  
Spectral Characteristics ◽  
Branching Ratio ◽  
Central Metal ◽  
X Ray ◽  
Cobalt Compounds ◽  
X Ray Absorption ◽  
Insight Into

The electronic structure of a material plays an important role in its functionality for different applications which can be probed using synchrotron-based spectroscopy techniques. Here, various cobalt-based compounds, differing in crystal structure, ligands surrounding the central metal ion and morphology, have been studied by soft X-ray absorption spectroscopy (XAS) at the CoL-edge in order to measure the effect of these parameters on the electronic structure. A careful qualitative analysis of the spectral branching ratio and relative intensities of theL3andL2peaks provide useful insight into the electronic properties of compounds such as CoO/Co(OH)2, CoCl2.6H2O/CoF2.4H2O, CoCl2/CoF2, Co3O4(bulk/nano/micro). For further detailed analysis of the XAS spectra, quantitative analysis has been performed by fitting the spectral profile with simulated spectra for a number of cobalt compounds using crystal field atomic multiplet calculations.

scholarly journals Enzymes of heme metabolism is the kidney. Regulation by trace metals which do not form heme complexes

1977 ◽  
Vol 146 (5) ◽  
pp. 1286-1293 ◽  
Author(s):  
MD Maines ◽  
A Kappas
Keyword(s):  
Metal Ions ◽  
Metal Ion ◽  
Early Period ◽  
Reciprocal Relationship ◽  
Central Metal ◽  
Ion Regulation ◽  
Heme Metabolism ◽  
Rate Limiting

The in vivo regulation by metal ions of the enzymes of heme metabolism in kidney-particularly of ALAS, the rate-limiting enzyme in heine formation- was investigated. Ni(2+) and Pt(4+), metals which do not enzymatically form metalloporphyrins, were found to regulate ALAS in kidney as they do in liver. The pattern of this regulation was generally similar to that observed with heme and metal ions in liver, i.e., a late increase in enzyme activity after an early period in which ALAS activity was unaltered or inhibited. The metals did not interact with the enzyme in vitro to alter its activity. In this study no direct reciprocal relationship between ALAS activity and total cellular heine content was demonstrated. The metal ions, particularly Pt(4+), also altered the activity of other enzymes of heme biosynthesis in kidney. Pt(4+) severely inhibited the activity of ALAD and UROS. Ni(2+) and Pt(4+) were potent inducers of heme oxygenase, the initial and rate-limiting enzyme in heine degradation. It is proposed that the physiological regulation of ALAS is mediated through the action of metal ions, rather than by the cellular content of heine, and that the regulation of ALAS by heine reflects the action of the central metal ion of heme rather than that of the entire metalloporphyrin complex. In this proposed mechanism for metal ion regulation of ALAS, the tetrapyrrole moiety of heine is considered to function principally as an efficient carrier of metal to the regulatory site for ALAS production, inasmuch as the tetrapyrrole ring itself has been shown in earlier studies not to have any effect on ALAS activity. The production of heine oxygenase is believed to be similarly regulated.

Electronic structures, spectroscopic properties, and reaction activities of porphyrins with alkali metal ions: density functional theory approach to the central metal effects

2012 ◽  
Vol 16 (07n08) ◽  
pp. 927-934 ◽  
Author(s):  
Luyang Zhao ◽  
Dongdong Qi ◽  
Lijuan Zhang ◽  
Ming Bai ◽  
Xue Cai
Keyword(s):  
Density Functional Theory ◽  
Alkali Metal ◽  
Metal Ions ◽  
Metal Ion ◽  
Density Functional ◽  
State Transitions ◽  
Theory Approach ◽  
Central Metal ◽  
Functional Theory ◽  
Molecular Stability

Density functional theory (DFT) calculation method was employed to investigate a series of nine alkali metal porphyrins (alk-Pors), namely HLiPor , HNaPor , HKPor , Li2Por , LiNaPor , LiKPor , Na2Por , NaKPor , and K2Por . These molecules show different configurations depending on different metal ions which locate over the central hole of the porphyrin ligand. Alk-Pors with larger-radius metal ion have smaller binding energy and thus is more difficult to keep stable. Further detailed molecular stability analysis was carried out by noncovalent interaction and electrostatic interaction via RDG and NBO charge distribution. UV-vis spectra of these nine compounds also show different spectral shapes depending on the central metals, and the dominant state transitions with high degeneracy are revealed to be influenced by high molecular symmetric order. Finally their difference in reactivity due to the electronegativity of central metals and the nature of porphyrin rings are predicted by electrostatic potential and Fukui functions.

scholarly journals Coordination properties of N,O-carboxymethyl chitosan (NOCC). Synthesis and equilibrium studies of some metal ion complexes. Ternary complexes involving Cu(II) with (NOCC) and some biorelevant ligand

2012 ◽  
Vol 10 (1) ◽  
pp. 59-70 ◽  
Author(s):  
Azza Shoukry ◽  
Wafaa Hosny
Keyword(s):  
Metal Ions ◽  
Stability Constants ◽  
Metal Ion ◽  
Ternary Complexes ◽  
Central Metal ◽  
Magnetic Studies ◽  
Complex Formation Equilibria ◽  
Equilibrium Studies ◽  
The Stability ◽  
Solid Complexes

AbstractIn the present study, the acid-base equilibria of N,O-carboxymethy chitosan abbreviated as (NOCC), is investigated. The complex formation equilibria with the metal ions Cu(II), Ni(II), Co(II), Mn(II), and Zn(II) are investigated potentiometrically. The stability constant values of the binary and ternary complexes formed in solution were determined and the binding centers of the ligands were assigned. The relationships between the properties of the studied central metal ions as ionic radius, electronegativity, atomic number, and ionization potential, and the stability constants of the formed complexes were investigated in an effort to give information about the nature of chemical bonding in complexes and make possible the calculation of unknown stability constants. Cu(II), Ni(II), and U(VI) complexes with NOCC are isolated as solid complexes and characterized by conventional chemical and physical methods. The structures of the isolated solid complexes are proposed on the basis of the spectral and magnetic studies. The ternary copper(II) complexes involving NOCC and various biologically relevant ligands containing different functional groups, as amino acids and DNA constituents are investigated. The stability constants of the complexes are determined and the concentration distribution diagrams of the complexes are evaluated.

Effect of solvent binding on UV-vis spectra and redox potentials of octaethylporphyrins containing first-row transition metal ions

2009 ◽  
Vol 13 (12) ◽  
pp. 1233-1242 ◽  
Author(s):  
Weihua Zhu ◽  
Xiaofeng Zhao ◽  
Zhongping Ou ◽  
Fan Zhou ◽  
Xiaohong Wang ◽  
...  
Keyword(s):  
Transition Metal ◽  
Metal Ions ◽  
Metal Ion ◽  
Binding Constants ◽  
Transition Metal Ions ◽  
Donor Number ◽  
Central Metal ◽  
Redox Potentials ◽  
Visible Spectra ◽  
Uv Visible

The UV-visible spectra and oxidation/reduction potentials for six octaethylporphyrins with first-row transition metal ions were measured in four non-aqueous solvents and then analyzed as a function of the Gutmann solvent parameters, donor number (DN) or acceptor number (AN). The utilized solvents were dichloromethane ( CH2Cl2 ), N, N-dimethylformamide (DMF), dimethyl sulfoxide (DMSO) and pyridine (py). The investigated porphyrins were (OEP)M, where OEP = the dianion of octaethylporphyrin and M = CoII, NiII, CuII, ZnII, FeIIICl or MnIIICl . UV-visible spectra upon solvent (S) binding to give (OEP)M(S) or [ (OEP)M(S)2]+Cl- were monitored during a titration of the porphyrin in CH2Cl2 and formation constants ( logβ n, n = 1 or 2) for the ligand addition reactions were determined using standard equations. Five-coordinate (OEP)CoII(S) and (OEP)ZnII(S) are generated in CH2Cl2 solutions containing DMF, DMSO or py while six-coordinate [ (OEP)Mn(S)2]+Cl and [ (OEP)Fe(S)2]+Cl- are formed under the same solution conditions. The magnitudes of the solvent binding constants are discussed in terms of both the solvent donor/acceptor properties and the electronegativity (EN) or stability index (SI) of the porphyrin central metal ion. A comparison between solvent binding constants measured in this study for (OEP)M and literature data for (TPP)M with the same central metal ions is presented.

PubChem and ChEMBL Beyond Lipinski

2019 ◽  
Author(s):  
Jean-Louis Reymond ◽  
Mahendra Awale ◽  
Daniel Probst ◽  
Alice Capecchi
Keyword(s):  
Nearest Neighbor ◽  
Molecular Shape ◽  
Biological Properties ◽  
Web Based ◽  
Large Molecules ◽  
Interactive Tools ◽  
Small Molecule Drugs ◽  
Pubchem Database ◽  
Nearest Neighbor Searches ◽  
Insight Into

<p>Seven million of the currently 94 million entries in the PubChem database break at least one of the four Lipinski constraints for oral bioavailability, 183,185 of which are also found in the ChEMBL database. These non-Lipinski PubChem (NLP) and ChEMBL (NLC) subsets are interesting because they contain new modalities that can display biological properties not accessible to small molecule drugs. Unfortunately, the current search tools in PubChem and ChEMBL are designed for small molecules and are not well suited to explore these subsets, which therefore remain poorly appreciated. Herein we report MXFP (macromolecule extended atom-pair fingerprint), a 217-D fingerprint tailored to analyze large molecules in terms of molecular shape and pharmacophores. We implement MXFP in two web-based applications, the first one to visualize NLP and NLC interactively using Faerun (http://faerun.gdb.tools/), the second one to perform MXFP nearest neighbor searches in NLP (http://similaritysearch.gdb.tools/). We show that these tools provide a meaningful insight into the diversity of large molecules in NLP and NLC. The interactive tools presented here are publicly available at http://gdb.unibe.ch and can be used freely to explore and better understand the diversity of non-Lipinski molecules in PubChem and ChEMBL.</p>

Use of agro-waste (Musa paradisiaca peels) as a sustainable biosorbent for toxic metal ions removal from contaminated water

2019 ◽  
Author(s):  
Chem Int
Keyword(s):  
Heavy Metal ◽  
Metal Ions ◽  
Contact Time ◽  
Metal Ion ◽  
Equilibrium Concentration ◽  
Ion Concentration ◽  
Contaminated Water ◽  
Musa Paradisiaca ◽  
Percentage Removal ◽  
Adsorbent Dose

A study of removal of heavy metal ions from heavy metal contaminated water using agro-waste was carried out with Musa paradisiaca peels as test adsorbent. The study was carried by adding known quantities of lead (II) ions and cadmium (II) ions each and respectively into specific volume of water and adding specific dose of the test adsorbent into the heavy metal ion solution, and the mixture was agitated for a specific period of time and then the concentration of the metal ion remaining in the solution was determined with Perkin Elmer Atomic absorption spectrophotometer model 2380. The effect of contact time, initial adsorbate concentration, adsorbent dose, pH and temperature were considered. From the effect of contact time results equilibrium concentration was established at 60minutes. The percentage removal of these metal ions studied, were all above 90%. Adsorption and percentage removal of Pb2+ and Cd2+ from their aqueous solutions were affected by change in initial metal ion concentration, adsorbent dose pH and temperature. Adsorption isotherm studies confirmed the adsorption of the metal ions on the test adsorbent with good mathematical fits into Langmuir and Freundlich adsorption isotherms. Regression correlation (R2) values of the isotherm plots are all positive (&gt;0.9), which suggests too, that the adsorption fitted into the isotherms considered.

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