Aptamers as Theranostic Agents: Modifications, Serum Stability and Functionalisation

Aptamers, and the selection process known as Systematic Evolution of Ligands by Exponential Enrichment (SELEX) used to generate them, were first described more than twenty years ago. Since then, there have been numerous modifications to the selection procedures. This review discusses the use of modified bases as a means of enhancing serum stability and producing effective therapeutic tools, as well as functionalising these nucleic acids to be used as potential diagnostic agents.

Synthesis, structural studies and catalytic activity of dioxidomolybdenum(VI) complexes with aroylhydrazones of naphthol-derivative

Reaction of the salicylhydrazone of 2-hydroxy-1-naphthaldehyde (H2L1), anthranylhydrazone of 2hydroxy-l-naphthaldehyde (H2L2), benzoylhydrazone of 2-hydroxy-1-acetonaphthone (H2L3) and anthranylhydrazone of 2-hydroxy-1-acetonaphthone (H2L4; general abbreviation H2L) with MoO2(acac)21 afforded a series of 5- and 6- coordinate Mo(VI) complexes of the type MoO2L1-2(ROH)] where R = C2H5 (1) and CH3 (2)], and MoO2L3-4] (3 and 4). The substrate binding capacity of 1 has been demonstrated by the formation of one mononuclear mixed-ligand dioxidomolybdenum complex MoO2L1(Q)] (where Q= gamma-picoline (la)). Molecular structure of all the complexes (I, la, 2,3 and 4) is determined by X-ray crystallography, demonstrating the dibasic tridentate behavior of ligands. All the complexes show two irreversible reductive responses within the potential window -0.73 to -1.08 V, due to Movl/Mov and Mov/Mow processes. Catalytic potential of these complexes was tested for the oxidation of benzoin using 30% aqueous H2O2 as an oxidant in methanol. At least four reaction products, benzoic acid, benzaldehydedimethylacetal, methyl benzoate and benzil were obtained with the 95-99% conversion under optimized reaction conditions. Oxidative bromination of salicylaldehyde, a functional mimic of haloperoxidases, in aqueous 1-1202/KEr in the presence of HC1O4 at room temperature has also been carried out successfully. (C) 2013 Elsevier Ltd. All rights reserved.

Modification of Extended Open Frameworks with Fluorescent Tags for Sensing Explosives: Competition between Size Selectivity and Electron Deficiency

Three new electron-rich metal-organic frameworks (MOF-1-MOF-3) have been synthesized by employing ligands bearing aromatic tags. The key role of the chosen aromatic tags is to enhance the -electron density of the luminescent MOFs. Single-crystal X-ray structures have revealed that these MOFs form three-dimensional porous networks with the aromatic tags projecting inwardly into the pores. These highly luminescent electron-rich MOFs have been successfully utilized for the detection of explosive nitroaromatic compounds (NACs) on the basis of fluorescence quenching. Although all of the prepared MOFs can serve as sensors for NACs, MOF-1 and MOF-2 exhibit superior sensitivity towards 4-nitrotoluene (4-NT) and 2,4-dinitrotoluene (DNT) compared to 2,4,6-trinitrotoluene (TNT) and 1,3,5-trinitrobenzene (TNB). MOF-3, on the other hand, shows an order of sensitivity in accordance with the electron deficiencies of the substrates. To understand such anomalous behavior, we have thoroughly analyzed both the steady-state and time-resolved fluorescence quenching associated with these interactions. Determination of static Stern-Volmer constants (K-S) as well as collisional constants (K-C) has revealed that MOF-1 and MOF-2 have higher K-S values with 4-NT than with TNT, whereas for MOF-3 the reverse order is observed. This apparently anomalous phenomenon was well corroborated by theoretical calculations. Moreover, recyclability and sensitivity studies have revealed that these MOFs can be reused several times and that their sensitivities towards TNT solution are at the parts per billion (ppb) level.

Optical bio-sensing devices based on etched fiber Bragg gratings coated with carbon nanotubes and graphene oxide along with a specific dendrimer

We demonstrate that etched fiber Bragg gratings (eFBGs) coated with single walled carbon nanotubes (SWNTs) and graphene oxide (GO) are highly sensitive and accurate biochemical sensors. Here, for detecting protein concanavalin A (Con A), mannose-functionalized poly(propyl ether imine) (PETIM) dendrimers (DMs) have been attached to the SWNTs (or GO) coated on the surface modified eFBG. The dendrimers act as multivalent ligands, having specificity to detect lectin Con A. The specificity of the sensor is shown by a much weaker response (factor of similar to 2500 for the SWNT and similar to 2000 for the GO coated eFBG) to detect non specific lectin peanut agglutinin. DM molecules functionalized GO coated eFBG sensors showed excellent specificity to Con A even in the presence of excess amount of an interfering protein bovine serum albumin. The shift in the Bragg wavelength (Delta lambda(B)) with respect to the lambda(B) values of SWNT (or GO)-DM coated eFBG for various concentrations of lectin follows Langmuir type adsorption isotherm, giving an affinity constant of similar to 4 x 10(7) M-1 for SWNTs coated eFBG and similar to 3 x 10(8) M-1 for the GO coated eFBG. (C) 2014 Elsevier B.V. All rights reserved.

Tuning nuclearity of clusters by positional change of functional group: Synthesis of polynuclear clusters, crystal structures and magnetic properties

Four neutral polynuclear magnetic clusters, (Mn6Mn2Na2I)-Mn-III-Na-II(N-3)(8)(mu(1)-O)(2)(L-1)(6)(CH3OH)(2)] (1), (Mn6Na2I)-Na-III(N-3)(4)(mu(4)-O)(2)(L-2)(4)(CH3COO)(4)] (2), Ni-5(II)(N-3)(4)(HL1)(4)(HCOO)(2)(CH3OH)(2)(H2O)(2)]center dot 2CH(3)OH (3) and (Ni4Na2I)-Na-II(N-3)(4)(HL2)(6)]center dot 2CH(3)OH (4) have been synthesized using tetradentate ligands H2L1-2 along with azide as a co-ligand. H2L1-2 are the products formed in situ upon condensation of 2-hydroxy-3-methoxybenzaldehyde with 1-aminopropan-2-ol and 1-aminopropan-3-ol, respectively. Single crystal X-ray diffraction and bond valence sum calculation showed that complex 1 is composed of both Mn-III and Mn-II. Complex 3 contains coordinated formate, which was formed upon in situ oxidation of methanol. The magnetic study over a wide range of temperatures of all the complexes (1-4) showed that 1 and 2 are antiferromagnetic whereas other two (3-4) are predominantly ferromagnetic. The estimated ground states of the complexes are S approximate to 3(1), S = 4(2), S = 5(3) and S approximate to 4(4), respectively. (C) 2014 Elsevier B.V. All rights reserved.

FOLD TYPE II PYRIDOXAL 5 `-PHOSPHATE DEPENDENT ENZYMES: STRUCTURE, SUBSTRATE RECOGNITION AND CATALYSIS

Enzymes utilizing pyridoxal 5'-phosphate dependent mechanism for catalysis are observed in all cellular forms of living organisms. PLP-dependent enzymes catalyze a wide variety of reactions involving amino acid substrates and their analogs. Structurally, these ubiquitous enzymes have been classified into four major fold types. We have carried out investigations on the structure and function of fold type I enzymes serine hydroxymethyl transferase and acetylornithine amino transferase, fold type n enzymes catabolic threonine deaminase, D-serine deaminase, D-cysteine desulfhydrase and diaminopropionate ammonia lyase. This review summarizes the major findings of investigations on fold type II enzymes in the context of similar studies on other PLP-dependent enzymes. Fold type II enzymes participate in pathways of both degradation and synthesis of amino acids. Polypeptide folds of these enzymes, features of their active sites, nature of interactions between the cofactor and the polypeptide, oligomeric structure, catalytic activities with various ligands, origin of specificity and plausible regulation of activity are briefly described. Analysis of the available crystal structures of fold type II enzymes revealed five different classes. The dimeric interfaces found in these enzymes vary across the classes and probably have functional significance.

Design and Synthesis of New Benzimidazole-Carbazole Conjugates for the Stabilization of Human Telomeric DNA, Telomerase Inhibition, and Their Selective Action on Cancer Cells

Cell-permeable small molecules that enhance the stability of the G-quadruplex (G4) DNA structures are currently among the most intensively pursued ligands for inhibition of the telomerase activity. Herein we report the design and syntheses of four novel benzimidazole carbazole conjugates and demonstrate their high binding affinity to G4 DNA. Si nuclease assay confirmed the ligand mediated G-quadruplex DNA protection. Additional evidence from Telomeric Repeat Amplification Protocol (TRAP-LIG) assay demonstrated efficient telomerase inhibition activity by the ligands. Two of the ligands showed IC50 values in the sub-micromolar range in the TRAP-LIG assay, which are the best among the benzimidazole derivatives reported so far. The ligands also exhibited cancer cell selective nuclear internalization, nuclear condensation, fragmentation, and eventually antiproliferative activity in long-term cell viability assays. Annexin V-FITC/PI staining assays confirm that the cell death induced by the ligands follows an apoptotic pathway. An insight into the mode of ligand binding was obtained from the molecular dynamics simulations.

DNA binders in clinical trials and chemotherapy

Cancer has always been a dreadful disease and continues to attract extensive research investigations. Various targets have been identified to restrain cancer. Among these DNA happens to be the most explored one. A wide variety of small molecules, often referred to as `ligands', has been synthesized to target numerous structural features of DNA. The sole purpose of such molecular design has been to interfere with the transcriptional machinery in order to drive the cancer cell toward apoptosis. The mode of action of the DNA targeting ligands focuses either on the sequence-specificity by groove binding and strand cleavage, or by identifying the morphologically distinct higher order structures like that of the G-quadruplex DNA. However, in spite of the extensive research, only a tiny fraction of the molecules have been able to reach clinical trials and only a handful are used in chemotherapy. This review attempts to record the journey of the DNA binding small molecules from its inception to cancer therapy via various modifications at the molecular level. Nevertheless, factors like limited bioavailability, severe toxicities, unfavorable pharmacokinetics etc. still prove to be the major impediments in the field which warrant considerable scope for further research investigations. (C) 2014 Published by Elsevier Ltd.

Oxovanadium(IV) complexes of curcumin for cellular imaging and mitochondria targeted photocytotoxicity

Oxovanadium(IV) complexes VO(R-tpy)(cur)](ClO4) (1, 2) of curcumin (Hcur) and terpyridine ligands (R-tpy) where R is phenyl (phtpy in 1) or p-triphenylphosphonium methylphenyl bromide (C6H4CH2PPh3Br) (TPP-phtpy in 2) were prepared and characterized and their DNA photocleavage activity, photocytotoxicity and cellular localization in cancer cells (HeLa and MCF-7) were studied. Acetylacetonate (acac) complexes VO(R-tpy)(acac)](ClO4) of phtpy (3) and TPP-phtpy (4) were prepared and used as the control species. These complexes showed efficient cleavage of pUC19 DNA in visible light of 454 nm and near-IR light of 705 rim. Complexes 1 and 2 showed significant photocytotoxicity in visible light of 400-700 nm. FACS analysis showed sub-G1/G0 phase cell-cycle arrest in cancer cells when treated with 1 and 2 in visible light in comparison with the dark controls. Fluorescence microscopic studies revealed specific localization of the p-triphenylphosphonium complex 2 in the mitochondria of MCF-7 cancer cells whereas no such specificity was observed for complex 1.

Characterizing the pocketome of Mycobacterium tuberculosis and application in rationalizing polypharmacological target selection

Polypharmacology is beginning to emerge as an important concept in the field of drug discovery. However, there are no established approaches to either select appropriate target sets or design polypharmacological drugs. Here, we propose a structural-proteomics approach that utilizes the structural information of the binding sites at a genome-scale obtained through in-house algorithms to characterize the pocketome, yielding a list of ligands that can participate in various biochemical events in the mycobacterial cell. The pocket-type space is seen to be much larger than the sequence or fold-space, suggesting that variations at the site-level contribute significantly to functional repertoire of the organism. All-pair comparisons of binding sites within Mycobacterium tuberculosis (Mtb), pocket-similarity network construction and clustering result in identification of binding-site sets, each containing a group of similar binding sites, theoretically having a potential to interact with a common set of compounds. A polypharmacology index is formulated to rank targets by incorporating a measure of druggability and similarity to other pockets within the proteome. This study presents a rational approach to identify targets with polypharmacological potential along with possible drugs for repurposing, while simultaneously, obtaining clues on lead compounds for use in new drug-discovery pipelines.

Component Selection in the Self-Assembly of Palladium(II) Nanocages and Cage-to-Cage Transformations

Dynamic supramolecular systems involving a tetratopic palladium(II) acceptor and three different pyridine-and imidazole-based donors have been used for self-selection by a synergistic effect of morphological information and coordination ability of ligands through specific coordination interactions. Three different cages were first synthesized by two-component self-assembly of individual donor and acceptor. When all four components were allowed to interact in a reaction mixture, only one out of three cages was isolated. The preferential binding affinity towards a particular partner was also established by transforming a non-preferred cage into a preferred cage by interaction with the appropriate ligand. Computational studies further supported the fact that coordination interaction of imidazole moiety to Pd-II is enthalpically more preferred compared to pyridine, which drives the selection process. Analysis of crystal packing of both complexes indicated the presence of strong hydrogen bonds between nitrate and water molecules and also H-bonded 3D networks of water. Both complexes exhibit promising proton conductivity (10(-5) to ca. 10(-3) Scm(-1)) at ambient temperature under a relative humidity of circa 98% with low activation energy.

Seeded-growth, nanocrystal-fusion, ion-exchange and inorganic-ligand mediated formation of semiconductor-based colloidal heterostructured nanocrystals

This article highlights different synthetic strategies for the preparation of colloidal heterostructured nanocrystals, where at least one component of the constituent nanostructure is a semiconductor. Growth of shell material on a core nanocrystal acting as a seed for heterogeneous nucleation of the shell has been discussed. This seeded-growth technique, being one of the most heavily explored mechanisms, has already been discussed in many other excellent review articles. However, here our discussion has been focused differently based on composition (semiconductor@semiconductor, magnet@semiconductor, metal@semiconductor and vice versa), shape anisotropy of the shell growth, and synthetic methodology such as one-step vs. multi-step. The relatively less explored strategy of preparing heterostructures via colloidal sintering of different nanostructures, known as nanocrystal-fusion, has been reviewed here. The ion-exchange strategy, which has recently attracted huge research interest, where compositional tuning of nanocrystals can be achieved by exchanging either the cation or anion of a nanocrystal, has also been discussed. Specifically, controlled partial ion exchange has been critically reviewed as a viable synthetic strategy for the fabrication of heterostructures. Notably, we have also included the very recent methodology of utilizing inorganic ligands for the fabrication of heterostructured colloidal nanocrystals. This unique strategy of inorganic ligands has appeared as a new frontier for the synthesis of heterostructures and is reviewed in detail here for the first time. In all these cases, recent developments have been discussed with greater detail to add upon the existing reviews on this broad topic of semiconductor-based colloidal heterostructured nanocrystals.

Metallacyclocumulenes: A Theoretical Perspective on the Structure, Bonding, and Reactivity

CONSPECTUS: Transition metals help to stabilize highly strained organic fragments. Metallacycles, especially unsaturated ones, provide much variety in this area. We had a sustained interest in understanding new C-C bond formation reactions affected by binuclear transition metal fragments Cp2M. One such study led to the exploration of the bimetallic C-C cleavage and coupled complexes, where the acetylide ligands bridge two metal atoms. The underlying M-C interaction in these complexes inspired the synthesis of a five-membered cyclocumulene complex, which opened a new phase in organometallic chemistry. The metallacyclocumulene produces a variety of C-C cleavage and coupled products including a radialene complex. Group 4 metallocenes have thus unlocked a fascinating chemistry by stabilizing strained unsaturated C4 organic fragments in the form of five-membered metallacyclocumulenes, metallacyclopentynes, and metallacycloallenes. Over the years, we have carried out a comprehensive theoretical study to understand the unusual stability and reactivity of these metallacycles. The unique (M-C-beta) interaction of the internal carbon atoms with the metal atom is the reason for unusual stability of the metallacycles. We have also shown that there is a definite dependence of the C-C coupling and cleavage reactions on the metal of metallacyclocumulenes. It demonstrates unexpected reaction pathways for these reactions. Based on this understanding, we have predicted and unraveled the stabilization factors of an unusual four-membered metallacycloallene complex. Indeed, our prediction about a four-membered heterometallacycle has led to an interesting bonding situation, which is experimentally realized. This type of M-C bonding is intriguing from a fundamental perspective and has great relevance in synthesizing unusual structures with interesting properties. In this Account, we first give a short prologue of what led to the present study and describe the salient features of the structure and bonding of the metallacyclocumulenes. The unusual reaction pathway of this metallacycle is explored next. Similar features of the metallacyclopentynes and metallacycloallenes are briefly mentioned. Then, we discuss the exploitation of the unique M-C bonding to design some exotic molecules such as a four-membered metallacycloallene complex. Our efforts to build a conceptual framework to understand these metallacycles and to exploit their chemistry continue.

The interaction of N-trifluoroacetylgalactosamine and its derivatives with winged bean (Psophocarpus tetragonolobus) basic agglutinin reveals differential mechanism of their recognition: a fluorine-19 nuclear magnetic resonance study

Here, we show the binding results of a leguminosae lectin, winged bean basic agglutinin (WBA I) to N-trifluoroacetylgalactosamine (NTFAGalN), methyl-alpha-N-trifluoroacetylgalactosamine (Me alpha NTFAGalN) and methyl-beta-tifluoroacetylgalactosamine (Me beta NTFAGalN) using (19) F NMR spectroscopy. No chemical shift difference between the free and bound states for NTFAGalN and Me beta NTFAGalN, and 0.01-ppm chemical shift change for Me alpha NTFAGalN, demonstrate that the Me alpha NTFAGalN has a sufficiently long residence time on the protein binding site as compared to Me beta NTFAGalN and the free anomers of NTFAGalN. The sugar anomers were found in slow exchange with the binding site of agglutinin. Consequently, we obtained their binding parameters to the protein using line shape analyses. Aforementioned analyses of the activation parameters for the interactions of these saccharides indicate that the binding of alpha and beta anomers of NTFAGalN and Me alpha NTFAGalN is controlled enthalpically, while that of Me beta NTFAGalN is controlled entropically. This asserts the sterically constrained nature of the interaction of the Me beta NTFAGalN with WBA I. These studies thus highlight a significant role of the conformation of the monosaccharide ligands for their recognition by WBA I.

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.