PocketMatch (version 2.0): A parallel algorithm for the detection of structural similarities between protein ligand binding-sites

Knowledge of protein-ligand interactions is essential to understand several biological processes and important for applications ranging from understanding protein function to drug discovery and protein engineering. Here, we describe an algorithm for the comparison of three-dimensional ligand-binding sites in protein structures. A previously described algorithm, PocketMatch (version 1.0) is optimised, expanded, and MPI-enabled for parallel execution. PocketMatch (version 2.0) rapidly quantifies binding-site similarity based on structural descriptors such as residue nature and interatomic distances. Atomic-scale alignments may also be obtained from amino acid residue pairings generated. It allows an end-user to compute database-wide, all-to-all comparisons in a matter of hours. The use of our algorithm on a sample dataset, performance-analysis, and annotated source code is also included.

Kinetically stabilized C-60-toluene solvate nanostructures with a discrete absorption edge enabling supramolecular topotactic molecular exchange

Nanosized fullerene solvates have attracted widespread research attention due to recent interesting discoveries. A particular type of solvate is limited to a fixed number of solvents and designing new solvates within the same family is a fundamental challenge. Here we demonstrate that the hexagonal closed packed (HCP) phase of C-60 solvates, formed with m-xylene, can also be stabilized using toluene. Contrary to the notion on their instability, these can be stabilized from minutes up to months by tuning the occupancy of solvent molecules. Due to high stability, we could record their absorption edge, and measure excitonic life-time, which has not been reported for any C-60 solvate. Despite being solid, absorbance spectrum of the solvates is similar in appearance to that of C-60 in solution. A new absorption band appears at 673 nm. The fluorescence lifetime at 760 nm is similar to 1.2 ns, suggesting an excited state unaffected by solvent-C-60 interaction. Finally, we utilized the unstable set of HCP solvates to exchange with a second solvent by a topotactic exchange mechanism, which rendered near permanent stability to the otherwise few minutes stable solvates. This is also the first example of topotactic exchange in supramolecular crystal, which is widely known in ionic solids. (C) 2014 Elsevier Ltd. All rights reserved.

Cu-II-Azide Polynuclear Complexes of Three Different Building Clusters with the Same Schiff-Base Ligand: Synthesis, Structures, Magnetic Behavior, and Density Functional Theory Studies

Three copper-azido complexes Cu-4(N-3)(8)(L-1)(2)(MeOH)(2)](n) (1), Cu-4(N-3)(8)(L-1)(2)] (2), and Cu-5(N-3)(10)(L-1)(2)](n) (3) L-1 is the imine resulting from the condensation of pyridine-2-carboxaldehyde with 2-(2-pyridyl)ethylamine] have been synthesized using lower molar equivalents of the Schiff base ligand with Cu(NO3)(2)center dot 3H(2)O and an excess of NaN3. Single crystal X-ray structures show that the basic unit of the complexes 1 and 2 contains Cu-4(II) building blocks; however, they have distinct basic and overall structures due to a small change in the bridging mode of the peripheral pair of copper atoms in the linear tetranudear structures. Interestingly, these changes are the result of changing the solvent system (MeOH/H2O to EtOH/H2O) used for the synthesis, without changing the proportions of the components (metal to ligand ratio 2:1). Using even lower proportions of the ligand, another unique complex was isolated with Cu-5(II) building units, forming a two-dimensional complex (3). Magnetic susceptibility measurements over a wide range of temperature exhibit the presence of both antiferromagnetic (very weak) and ferromagnetic exchanges within the tetranuclear unit structures. Density functional theory calculations (using B3LYP functional, and two different basis sets) have been performed on the complexes 1 and 2 to provide a qualitative theoretical interpretation of their overall magnetic behavior.

Stabilization of Co-3 - Oxoclusters in a pcu Net: Synthesis, Structure, Solvent Exchange (Single Crystal to Single Crystal) and Magnetic Studies

The solvothermal reaction of CoCl(2)4H(2)O and 4,4-sulfonyldibenzoic acid (H(2)SDBA) resulted in the formation of a three-dimensional coordination polymer Co-3(C14H8O6S)(3)(DMA)(2)(MeOH)].DMA (Ia) consisting of trinuclear Co-3 oxo-cluster units. The Co-3 trimeric units are connected by SDBA(2-) anions leading to a three dimensional structure with a pcu topology. The terminal methanol molecules could be exchanged in a single crystal to single crystal (SCSC) fashion by other similar solvent molecules (ethanol, acetonitrile, water, ethyleneglycol). Magnetic studies on the parent compound, Ia, indicate antiferromagnetic interactions between the central metal atoms.

Structural diversity and ligand specificity of lectins. The Bangalore effort

Structural studies in this laboratory encompass four of the five major classes of plant lectins, including the one discovered by us. In addition to addressing issues specific to individual lectins, the work provided insights into protein folding, quaternary association and generation of ligand specificity. Legume and beta-prism fold lectins constitute families of proteins in which small alterations in essentially the same tertiary structure lead to large variations in quaternary structure, including that involving an open structure. Strategies for generating ligand specificity include water bridges, variation in loop length, post translational modification and oligomerization. Three of the structural classes investigated have subunits with three-fold symmetry. The symmetry in the structure is reflected in the sequence to different extents in different subclasses. The evolutionary implications of this observation have been explored. The work on lectins has now been extended to those from mycobacteria.

Exchange bias in strained SrRuO3 thin films

Recently, it was found that the ferromagnetic SrRuO3 when combined with another ferromagnet in thin film form gives rise to exchange bias (EB) effect. However, we observed EB in single, strained, SrRuO3 thin films grown on diamagnetic LaAlO3 (100) substrates. It displays the training effect, which essentially confirms EB. The temperature dependence of the EB reveals the blocking temperature to be around similar to 75 K. The strength of the exchange bias decreases with the increase in thickness of the film. We observe tensile strain in the out of plane direction. Further, the presence of in-plane compressive strain is observed through asymmetric reciprocal space mapping. Finally, we find a direct link between strain and EB. The evolution of strain with thickness matches well with the nature of scaled EB. It has been shown earlier by first principle calculations that this strain can induce EB in thin films. (C) 2014 AIP Publishing LLC.

Synthesis and crystal structure of copper (II) uracil ternary polymeric complex with 1,10-phenanthroline along with the Hirshfeld surface analysis of the metal binding sites for the uracil ligand

The study of models for ``metal-enzyme-substrate'' interaction has been a proactive area of research owing to its biological and pharmacological importance. In this regard the ternary copper uracil complex with 1,10-phenanthroline represents metal-enzyme-substrate system for DNA binding enzymes. The synthesis of the complex, followed by slow evaporation of the reaction mixture forms two concomitant solvatomorph crystals viz., {Cu(phen)(mu-ura)(H2O)](n)center dot H2O (1a)} and {Cu(phen)(mu-ura)(H2O)](n)center dot CH3OH (1b)}. Both complexes are structurally characterized, while elemental analysis, IR and EPR spectra were recorded for 1b (major product). In both complexes, uracil coordinates uniquely via N1 and N3 nitrogen atom acting as a bidentate bridging ligand forming a 1-D polymer. The two solvatomorphs were quantitatively analyzed for the differences with the aid of Hirshfeld surface analysis. (C) 2014 Elsevier B.V. All rights reserved.

2-(Phenylazo)pyridineplatinum(II) Catecholates Showing Photocytotoxicity, Nuclear Uptake, and Glutathione-Triggered Ligand Release

Platinum(II) complexes Pt(pap)(an-cat)] (1) and Pt(pap)(py-cat)] (2) with 2-(phenylazo)pyridine (pap), 4-2-(anthracen-9-ylmethylene)amino]ethyl]benzene-1,2-diol (H(2)an-cat), and 4-2-(pyren-1-ylmethylene)amino]ethyl]benzene-1,2-diol (H2py-cat) were prepared, and their photoinduced cytotoxicity was studied. The complexes were found to release catecholate ligand in the presence of excess glutathione (GSH), resulting in cellular toxicity in the cancer cells. The catecholate complex Pt(pap)(cat)] (3) was prepared and used as a control. Complex 3, which is structurally characterized by X-ray crystallography, has platinum(II) in a distorted square-planar geometry. The complexes are redox-active, showing responses near 0.6 and 1.0 V versus SCE in N,N-dimethylformamide/0.1 M tetrabutylammonium perchlorate corresponding to a two-step catechol oxidation process and at -0.3 and -1.3 V for reduction of the pap ligand. Complex 1 showed remarkable light-induced cytotoxicity in HaCaT (human skin keratinocytes) and MCF-7 (human breast cancer) cells, giving IC50 value of similar to 5 mu M in visible light of 400-700 nm and >40 mu M in the dark. The 2',7'-dichlorofluorescein diacetate (DCFDA) assay showed the generation of reactive oxygen species (ROS), which seems to trigger apoptosis, as is evident from the annexin V-fluorescein isothiocyanate (FITC)/propidium iodide (PI) assay. The fluorescence microscopic images showed significant nuclear localization of the complexes and free ligands. A mechanistic study revealed possible reduction of the coordinated azo bond of pap by cellular GSH, releasing the catecholate ligand and resulting in remarkable photochemotherapeutic action of the complexes.

Ligand 5,10,15,20-Tetra(N-methyl-4-pyridyl)porphine (TMPyP4) Prefers the Parallel Propeller-Type Human Telomeric G-Quadruplex DNA over Its Other Polymorphs

The binding of ligand 5,10,15,20-tetra(N-methyl-4-pyridyl)porphine (TMPyP4) with telomeric and genomic G-quadruplex DNA has been extensively studied. However, a comparative study of interactions of TMPyP4 with different conformations of human telomeric G-quadruplex DNA, namely, parallel propeller-type (PP), antiparallel basket-type (AB), and mixed hybrid-type (MH) G-quadruplex DNA, has not been done. We considered all the possible binding sites in each of the G-quadruplex DNA structures and docked TMPyP4 to each one of them. The resultant most potent sites for binding were analyzed from the mean binding free energy of the complexes. Molecular dynamics simulations were then carried out, and analysis of the binding free energy of the TMPyP4-G-quadruplex complex showed that the binding of TMPyP4 with parallel propeller-type G-quadruplex DNA is preferred over the other two G-quadruplex DNA conformations. The results obtained from the change in solvent excluded surface area (SESA) and solvent accessible surface area (SASA) also support the more pronounced binding of the ligand with the parallel propeller-type G-quadruplex DNA.

Jacalin-carbohydrate interactions: distortion of the ligand molecule as a determinant of affinity

Jacalin is among the most thoroughly studied lectins. Its carbohydrate-binding site has also been well characterized. It has been postulated that the lower affinity of beta-galactosides for jacalin compared with beta-galactosides is caused by steric interactions of the substituents in the former with the protein. This issue has been explored energetically and structurally using different appropriate carbohydrate complexes of jacalin. It turns out that the earlier postulation is not correct. The interactions of the substituent with the binding site remain essentially the same irrespective of the anomeric nature of the substitution. This is achieved through a distortion of the sugar ring in beta-galactosides. The difference in energy, and therefore in affinity, is caused by a distortion of the sugar ring in beta-galactosides. The elucidation of this unprecedented distortion of the ligand as a strategy for modulating affinity is of general interest. The crystal structures also provide a rationale for the relative affinities of the different carbohydrate ligands for jacalin.

Remarkable visible light-triggered cytotoxicity of mitochondria targeting mixed-ligand cobalt(III) complexes of curcumin and phenanthroline bases binding to human serum albumin

Six new mixed-ligand cobalt(III) complexes of formulation Co(N-N)(2)(O-O)](ClO4)(2) (1-6), where N-N is a N,N-donor phenanthroline base, namely, 1,10-phenanthroline (phen in 1, 2), dipyrido3,2-d:2',3'-f] quinoxaline (dpq in 3, 4), and dipyrido3,2-a:2',3'-c]phenazine (dppz in 5, 6), O-O is acetylacetonate (acac in 1, 3, 5) or curcumin (bis(4-hydroxy-3-methoxyphenyl)-1,6-diene-3,5-dione, cur in 2, 4, 6), have been synthesized and characterized. The X-ray crystal structures of complex 1 (as PF6- salt, 1a) and 3 show distorted octahedral geometries formed by the CoN4O2 core. The complexes 1, 3 and 5 having the simple acac ligand are prepared as control species to understand the role of curcumin. The optimized geometries and the frontier orbitals of the curcumin complexes 2, 4, and 6 are obtained from the DFT calculations. The complexes 2, 4, and 6 having the photoactive curcumin moiety display an absorption band in the visible region near 420 nm and show remarkable photocytotoxicity in HeLa cancer cells with respective IC50 values of 7.4 mu M, 5.1 mu M and 1.6 mu M while being much less toxic in dark. MTT assay using complex 6 shows that it is not significantly photocytotoxic to MCF-10A normal cells. The control complexes having the acac ligand are non-toxic both in the presence and absence of light. The cell death is apoptotic in nature and triggered by the photogeneration of reactive oxygen species. Fluorescence imaging experiments on HeLa cells reveals that complex 6 accumulated primarily inside the mitochondria. Human serum albumin (HSA) binding experiments show that the complexes bind HSA with good affinity, but 6 binds with the highest affinity, with a K-b value of 9.8 x 10(5) M-1. Thus, complex 6 with its negligible toxicity in the dark and in normal cells but remarkable toxicity in visible light holds significant photochemotherapeutic potential.

Significant photocytotoxic effect of an iron(III) complex of a Schiff base ligand derived from vitamin B-6 and thiosemicarbazide in visible light

Iron(III)-Schiff base complexes, namely, Fe(tsc-py)(2)](NO3) (1), Fe(tsc-acpy)(2)](NO3) (2) and Fe(tsc-VB6)(2)](NO3) (3), where tsc-py, tsc-acpy and tsc-VB6 are the respective Schiff bases derived from thiosemicarbazide (tsc) and pyridine-2-aldehyde (tsc-py), 2-acetyl pyridine (tsc-acpy) and vitamin B-6 (pyridoxal, tsc-VB6), have been prepared, structurally characterized and their photocytotoxicity studied in cancer HeLa cells. The single crystal X-ray structures of the complexes 1 and 2 show a distorted octahedral geometry formed by the FeN4S2 core. The low-spin and 1 : 1 electrolytic complexes display a broad absorption band in the visible region. Complexes 1 and 2, without any VB6 moiety are not cytotoxic under light or dark conditions. Complex 3 is significantly photocytotoxic under visible light of 400-700 nm giving an IC50 value of 22.5 mu M in HeLa cells with no dark toxicity (IC50 > 100 mu M). The photo-induced cell death is attributable to apoptotic pathways involving photo-assisted generation of intracellular ROS. The observed photocytotoxicity of complex 3 could be the result of its better photosensitizing property combined with its enhanced uptake into cancer cells via a VB6 transporting membrane carrier (VTC) mediated diffusion pathway due to the presence of the VB6 moiety compared to the two non-vitamin B-6 analogues, complexes 1 and 2.

First hyperpolarizability of Ru-half-sandwich complexes: The effect of halogen atom substitution on the ancillary ligand

The first hyperpolarizability (beta) of a series of half-sandwich Ru complexes with a mercaptobenzothiazole ligand bearing a halogen atom substitution in the para-position has been investigated by hyper-Rayleigh scattering and quantum chemical calculations. The heterocyclic ligand with a bromine atom in the para position makes it a very good donor and charge flows to the Ru center enhancing the beta value of the complex by a factor of 2 compared to the complex with the ligand without the halogen substitution. The resonance (+R) and the inductive (-I) effects exerted by the halogen atom in the para position push electrons in opposing directions in the complex. For the Br and Cl atoms the resonance effect dominates which enables the ligand to donate electrons to the metal center thereby increasing the hyperpolarizability whereas for the fluorine atom, the inductive effect is dominant which reduces the charge flow to the metal and the hyperpolarizability drops even below that of the unsubstituted ligand. This unprecedented halogen atom effect on beta of metal complexes is reported. (C) 2015 Elsevier By. All rights reserved.