Metal-Free Activation of Molecular Oxygen by Quaternary Ammonium-Based Ionic Liquid: A Detail Mechanistic Study.

Most oxidation processes in common organic synthesis and chemical biology require transition metal catalysts or metalloenzymes. Herein, we report a detailed mechanistic study of a metal-free oxygen (O2) activation protocol on benzylamine/alcohols using simple quaternary alkylammonium-based ionic liquids to produce products such as amide, aldehyde, imine, and in some cases, even aromatized products. NMR and various control experiments established the product formation and reaction mechanism, which involved the conversion of molecular oxygen into a hydroperoxyl radical via a proton-coupled electron transfer process. Detection of hydrogen peroxide in the reaction medium using colorimetric analysis supported the proposed mechanism of oxygen activation. Furthermore, first-principles calculations using density functional theory (DFT) revealed that reaction coordinates and transition state spin densities have a unique spin conversion of triplet oxygen leading to formation of singlet products via a minimum energy crossing point. In addition to DFT, domain-based local pair natural orbital coupled cluster, (DLPNO-CCSD(T)), and complete active space self-consistent field, CASSCF(20,14) methods complemented the above findings. Partial density of states analysis showed stabilization of π* orbital of oxygen in the presence of ionic liquid, making it susceptible to hydrogen abstraction in a mild, metal-free condition. Inductively coupled plasma atomic emission spectroscopic (ICP-AES) analysis of reactant and ionic liquids clearly showed the absence of any significant transition metal contamination. The current results described the origin of O2 activation within the context of molecular orbital (MO) theory and opened up a new avenue for the use of ionic liquids as inexpensive, multifunctional and high-performance alternative to metal-based catalysts for O2 activation.

Newly Synthesized 3-Indolyl Furanoid Inhibits Matrix Metalloproteinase-9 Activity and Prevents Nonsteroidal Anti-inflammatory Drug-Induced Gastric Ulceration.

Indomethacin, a known nonsteroidal anti-inflammatory drug (NSAID) induces gastric inflammation, causing degradation of the extracellular matrix by specific matrix metalloproteinases (MMPs). We investigated the antiulcer efficacy of 3-indolyl furanoids (3g and 3c, i.e., methoxy substitution at 4- and 5-positions of the indole ring, respectively), derived from indomethacin. Interestingly, 3g protected against indomethacin-induced gastropathy in vivo by inhibiting MMP-9. Our work established a chemical modification strategy for the development of safer NSAIDs. Moreover, in vitro and in silico studies confirmed that 3g inhibited MMP-9 activity with an IC50 value of 50 µM by binding to the catalytic cleft of MMP-9, leading to ulcer prevention. Pharmacokinetics was presented as the mean concentration-time profile in the rat plasma, and the extraction efficiency was greater than 70%, showing a Cmax of 104.48 µg/mL after 6.0 h (tmax) treatment with half-life and area under the curve being 7.0 h and 1273.8 h µg/mL, respectively, indicating the higher antiulcer potency of 3g.

Modulatory role of copper on hIAPP aggregation and toxicity in presence of insulin.

Aggregation of the human islets amyloid polypeptide, or hIAPP, is linked to ß-cell death in type II diabetes mellitus (T2DM). Different pancreatic ß-cell environmental variables such as pH, insulin and metal ions play a key role in controlling the hIAPP aggregation. Since insulin and hIAPP are co-secreted, it is known from numerous studies that insulin suppresses hIAPP fibrillation by preventing the initial dimerization process. On the other hand, zinc and copper each have an inhibitory impact on hIAPP fibrillation, but copper promotes the production of toxic oligomers. Interestingly, the insulin oligomeric equilibrium is controlled by the concentration of zinc ions when the effect of insulin and zinc has been tested together. Lower zinc concentrations cause the equilibrium to shift towards the monomer and dimer states of insulin, which bind to monomeric hIAPP and stop it from developing into a fibril. On the other hand, the combined effects of copper and insulin have not yet been studied. In this study, we have demonstrated how the presence of copper affects hIAPP aggregation and the toxicity of the resultant conformers with or without insulin. For this purpose, we have used a set of biophysical techniques, including NMR, fluorescence, CD etc., in combination with AFM and cell cytotoxicity assay. In the presence and/or absence of insulin, copper induces hIAPP to form structurally distinct stable toxic oligomers, deterring the fibrillation process. More specifically, the oligomers generated in the presence of insulin have slightly higher toxicity than those formed in the absence of insulin. This research will increase our understanding of the combined modulatory effect of two ß-cell environmental factors on hIAPP aggregation.

Exploring structural features and potential lipid interactions of Pseudomonas aeruginosa type three secretion effector PemB by spectroscopic and calorimetric experiments.

Type Three Secretion System (T3SS) is a sophisticated nano-scale weapon utilized by several gram negative bacteria under stringent spatio-temporal regulation to manipulate and evade host immune systems in order to cause infection. To the best of our knowledge, this present study is the first report where we embark upon characterizing inherent features of native type three secretion effector protein PemB through biophysical techniques. Herein, first, we demonstrate binding affinity of PemB for phosphoinositides through isothermal calorimetric titrations. Second, we shed light on its strong homo-oligomerization propensity in aqueous solution through multiple biophysical methods. Third, we also employ several spectroscopic techniques to delineate its disordered and helical conformation. Lastly, we perform a phylogenetic analysis of this new effector to elucidate evolutionary relationship with other organisms. Taken together, our results shall surely contribute to our existing knowledge of Pseudomonas aeruginosa secretome.

Omeprazole prevents stress induced gastric ulcer by direct inhibition of MMP-2/TIMP-3 interactions.

The healing of damaged tissues in gastric tract starts with the extracellular matrix (ECM) remodeling by the action of matrix metalloproteinases (MMPs). Particularly, MMP-2 (gelatinase-A) maintains ECM structure and function by degrading type IV collagen, the major component of basement membranes and by clearing denatured collagen. The proteolytic activities of MMPs are critically balanced by endogenous tissue inhibitors of metalloproteinases (TIMPs) and disruption of this balance results in several diseases. The well-known drug omeprazole is a proton pump inhibitor used for curing gastric ulcer. However, the action of omeprazole in ECM remodeling on gastroprotection has never been explored. Herein, using rat model of gastric ulcer, we report that restraint cold stress caused increase apoptosis to surface epithelia of gastric tissues along with TIMP-3 upregulation and inhibition of MMP-2 activity thereon. In contrast, omeprazole treatment suppressed TIMP-3 while increasing MMP-2 activity and thereby, restoring MMP-2/TIMP-3 balance. Additionally, nanomolar binding constant (Kd = 318 nM) of omeprazole with purified MMP-2 indicates a direct effect of omeprazole in restoring MMP-2 activity. Further in silico simulations revealed a plausible mechanism of action of omeprazole for TIMP-3 deactivation. Altogether, omeprazole restores MMP-2 activity and reduces apoptosis while preventing acute stress-induced gastric ulcer that occurs via suppression of nuclear factor kappa B (NF-κB) activity and peroxisome proliferator-activated receptor gamma activity (PPAR-γ). This represents an unprecedented correlation between physical docking of drug molecule to a protease and the severity of organ injury and provides a novel therapeutic approach to prevent stress induced tissue damage.

Synthesis of N-Fused Triazole-Piperazine-Quinazolinones via One-Pot Tandem Click Reaction and Cross-Dehydrogenative Coupling.

Herein, a one-pot protocol to synthesize tetracyclic triazole-piperazine-quinazolinone-fused N-heterocyclic scaffolds is reported. In this strategy, a tandem approach of two highly efficient synthetic reactions, click and cross-dehydrogentive coupling reactions, with high atom economy were employed to obtain the target N-fused scaffolds. Being highly functional group tolerable, this method has broad substrate scope. Interestingly, some of these derivatives showed strong white solid-state fluorescence.

Deciphering the structural intricacy in virulence effectors for proton-motive force mediated unfolding in type-III protein secretion.

Given that the protein unfolding requisite for type-III secretion system (T3SS)-mediated secretion is an energetically unfavorable process, the question of how do pathogenic bacteria unfold and secrete hundreds of toxic proteins in seconds remain largely unknown. In this study, a systematic effort combining experimental and computational approaches has been employed to get some mechanistic insights on the unfolding of effectors in T3SS secretion. The in-depth analysis of pH-dependent folding and stability of a T3SS effector ExoY revealed that proton-concentration gradient (~pH 5.8-6.0) generated by proton-motive force (PMF) had significantly affected folding and structural stability of this protein without significant loss of the free energy of unfolding. Importantly, the lower energetic cost associated with the global unfolding of ExoY was mainly due to its inherent stereo-chemical frustrations embedded within its native-like structure as observed from its core structural analysis. These observations suggest that the cooperation between the evolved structural features of ExoY and pH-mediated unfolding is crucial for PMF-mediated T3SS secretion. From a comprehensive computational analysis of 371 T3SS effectors it was concluded that many of these effectors belong to the category of intrinsically disordered proteins (IDPs) and have similar conserved structural archetypes to facilitate early-stage unfolding process as observed in ExoY. We had also provided details of folding, stability, and molecular evolution in T3SS effectors and established the role of evolved structural archetypes in early-stage unfolding events of this effector for maintaining balance in secretion and function trade-off.

Solvent-Assisted Tyrosine-Based Dipeptide Forms Low-Molecular Weight Gel: Preparation and Its Potential Use in Dye Removal and Oil Spillage Separation from Water.

Low-molecular weight gelators (supramolecular, or simply molecular gels) are highly important molecular frameworks because of their potential application in drug delivery, catalysis, pollutant removal, sensing materials, and so forth. Herein, a small dipeptide composed of N-(tert-butoxycarbonyl)pentafluoro-l-phenylalanine and O-benzyl-l-tyrosine methyl ester was synthesized, and its gelation ability was investigated in different solvent systems. It was found that the dipeptide was unable to form gel with a single solvent, but a mixture of solvent systems was found to be suitable for the gelation of this dipeptide. Interestingly, water was found to be essential for gelation with the polar protic solvent, and long-chain hydrocarbon units such as, petroleum ether, kerosene, and diesel, were important for gelation with aromatic solvents. The structural insights of these gels were characterized by field-emission scanning electronic microscopy, atomic force microscopy, Fourier transform infrared analysis, and X-ray diffraction studies, and their mechanical strengths were characterized by rheological experiments. Both of the gels obtained from these two solvent systems were thermoreversible in nature, and these translucent gels had potential application for the treatment of waste water. The gel obtained from dipeptides with methanol-water was used to remove toxic dyes (crystal violet, Eriochrome Black T, and rhodamine B) from water. Furthermore, the gel obtained from dipeptide with assistance from toluene-petroleum ether was used as a phase-selective gelator for oil-spill recovery.

Curcumin stably interacts with DNA hairpin through minor groove binding and demonstrates enhanced cytotoxicity in combination with FdU nucleotides.

We report, based on biophysical studies and molecular mechanical calculations that curcumin binds DNA hairpin in the minor groove adjacent to the loop region forming a stable complex. UV-Vis and fluorescence spectroscopy indicated interaction of curcumin with DNA hairpin. In this novel binding motif, two É£ H of curcumin heptadiene chain are closely positioned to the A16-H8 and A17-H8, while G12-H8 is located in the close proximity of curcumin α H. Molecular dynamics (MD) simulations suggest, the complex is stabilized by noncovalent forces including; π-π stacking, H-bonding and hydrophobic interactions. Nuclear magnetic resonance (NMR) spectroscopy in combination with molecular dynamics simulations indicated curcumin is bound in the minor groove, while circular dichroism (CD) spectra suggested minute enhancement in base stacking and a little change in DNA helicity, without significant conformational change of DNA hairpin structure. The DNA:curcumin complex formed with FdU nucleotides rather than Thymidine, demonstrated enhanced cytotoxicity towards oral cancer cells relative to the only FdU substituted hairpin. Fluorescence co-localization demonstrated stability of the complex in biologically relevant conditions, including its cellular uptake. Acridine orange/EtBr staining further confirmed the enhanced cytotoxic effects of the complex, suggesting apoptosis as mode of cell death. Thus, curcumin can be noncovalently complexed to small DNA hairpin for cellular delivery and the complex showed increased cytotoxicity in combination with FdU nucleotides, demonstrating its potential for advanced cancer therapy.

Silver-catalysed azide-alkyne cycloaddition (AgAAC): assessing the mechanism by density functional theory calculations.

'Click reactions' are the copper catalysed dipolar cycloaddition reaction of azides and alkynes to incorporate nitrogens into a cyclic hydrocarbon scaffold forming a triazole ring. Owing to its efficiency and versatility, this reaction and the products, triazole-containing heterocycles, have immense importance in medicinal chemistry. Copper is the only known catalyst to carry out this reaction, the mechanism of which remains unclear. We report here that the 'click reactions' can also be catalysed by silver halides in non-aqueous medium. It constitutes an alternative to the well-known CuAAC click reaction. The yield of the reaction varies on the type of counter ion present in the silver salt. This reaction exhibits significant features, such as high regioselectivity, mild reaction conditions, easy availability of substrates and reasonably good yields. In this communication, the findings of a new catalyst along with the effect of solvent and counter ions will help to decipher the still obscure mechanism of this important reaction.

Molecular Details of Acetate Binding to a New Diamine Receptor by NMR and FT-IR Analyses.

Acetate anion plays an important role in several biochemical functions such as enzyme reaction, antibody response, and action of receptor molecules. This investigation reports the synthesis and molecular details of a unique receptor, 2-amino-N-(2-amino-benzyl)-benzamide (R) that senses selectively acetate via simultaneous involvement of one aromatic amine group and an amide proton of the receptor molecule. Solution-state NMR, steady-state fluorescence, and FT-IR examinations established that the acetate anion binds to the receptor with 1:1 ratio with high specificity. The binding was stabilized by two H-bond formations between the oxygen atoms of acetate anion and two H atoms, one from amide group and the other from the amine group of the receptor. The binding interaction caused significant changes in the chemical shift of the receptor protons, and the evaluated affinity constant, from the NMR measurements, was found to be 1.87 × 10(4) M(-1). Density functional theory (DFT) analysis further showed a significant rotation of one of the two aromatic rings leading to formation of a 10-member ring involving the acetate anion, amide proton, and the one amine group attached to aromatic ring. The H-bond patterns observed in the crystal structure were significantly changed due to complex formation. However, the changes in the geometrical arrangement in the complex caused a small but significant increase of the fluorescence emission. Acetate geometry and unique positioning of the amide and amine groups of the receptor render the recognition feasible, and DFT analysis estimated ∼30 kJ M(-1) stabilization due to 1:1 complexation. Such positioning and geometrical arrangement may make the receptor very specific to bind acetate anion, and as such R became a very relevant molecule in detection and function of the acetate anion present in complex biochemical systems.

Binding interaction of a novel fluorophore with serum albumins: steady state fluorescence perturbation and molecular modeling analysis.

Fluorescence emission and anisotropy are widely used to measure the binding parameters and kinetic behavior of reactions that cause a change in the rotational time of a fluorescent molecule. We report here fluorescence emission and anisotropy behavior of a newly synthesized novel naphthalene base fluorophore (methyl 3-[(6-{[2-(tert-butoxy)-2-oxoethyl] (4-methoxyphenyl)amino}naphthalen-2-yl)formamido]propanoate) in several solution conditions including its binding to human and bovine serum albumin proteins both in their native and denatured states. The fluorescence yield of the compound substantially increased inside hydrophobic protein surface and ~30 nm decrease in Stokes' shift, compared to aqueous solution, was observed. Shift in fluorescence excitation peak position from the absorption peak of the molecule was ~8 nm in protein solution. This indicated possible alteration of excited state geometry of the compound by the globular fold of albumins. In addition, we measured the steady state fluorescence anisotropy of the molecule to evaluate several thermodynamic parameters and the results suggested the binding was energetically favorable. The measured ΔG° was ~-30 kJ mol(-1) and the derived dissociation constant was ~10(-6) M. The molecular docking analysis further highlighted the nonspecific association of the compound with the proteins and hydrophobic forces may have a significant role in the binding processes. Under the denatured condition of the protein, the compound lost its binding efficacy and reduction in fluorescence intensity was observed. Thus, the molecule appears as a new fluorescence probe to report the nature of its binding site in terms of increased fluorescence quantum yield and decreased Stokes' shift. It can also report the changes in the binding site due to global change in protein structure such as unfolding/misfolding often linked to several human disorder. Further it could be useful to detect and study the drug binding site of specific protein of interest.

Cα-H carries information of a hydrogen bond involving the geminal hydroxyl group: a case study with a hydrogen-bonded complex of 1,1,1,3,3,3-hexafluoro-2-propanol and tertiary amines.

Experimental measurement of the contribution of H-bonding to intermolecular and intramolecular interactions that provide specificity to biological complex formation is an important aspect of macromolecular chemistry and structural biology. However, there are very few viable methods available to determine the energetic contribution of an individual hydrogen bond to binding and catalysis in biological systems. Therefore, the methods that use secondary deuterium isotope effects analyzed by NMR or equilibrium or kinetic isotope effect measurements are attractive ways to gain information on the H-bonding properties of an alcohol system, particularly in a biological environment. Here, we explore the anharmonic contribution to the C-H group when the O-H group of 1,1,1,3,3,3-hexafluoro-2-propanol (HFP) forms an intermolecular H-bond with the amines by quantum mechanical calculations and by experimentally measuring the H/D effect by NMR. Within the framework of density functional theory, ab initio calculations were carried out for HFP in its two different conformational states and their H-bonded complexes with tertiary amines to determine the (13)C chemical shielding, change in their vibrational equilibrium distances, and the deuterium isotope effect on (13)C2 (secondary carbon) of HFP upon formation of complexes with tertiary amines. When C2-OH was involved in hydrogen bond formation (O-H as hydrogen donor), it weakened the geminal C2-H bond; it was reflected in the NMR chemical shift, coupling constant, and the equilibrium distances of the C-H bond. The first derivative of nuclear shielding at C2 in HFP was -48.94 and -50.73 ppm Å(-1) for anti and gauche conformations, respectively. In the complex, the values were -50.28 and -50.76 ppm Å(-1), respectively. The C-H stretching frequency was lower than the free monomer, indicating enhanced anharmonicity in the C-H bond in the complex form. In chloroform, HFP formed a complex with the amine; δC2 was 69.107 ppm for HFP-triethylamine and 68.766 ppm for HFP-d2-triethylamine and the difference in chemical shift, the ΔδC2 was 341 ppb. The enhanced anharmonicity in the hydrogen-bonded complex resulted in a larger vibrational equilibrium distance in C-H/D bonds. An analysis with the Morse potential function indicated that the enhanced anharmonicity encountered in the bond was the origin of a larger isotope effect and the equilibrium distances. Change in vibrational equilibrium distance and the deuterium isotope effect, as observed in the complex, could be used as parameters in monitoring the strength of the H-bond in small model systems with promising application in biomacromolecules.

Potent anticancer activity of cystine-based dipeptides and their interaction with serum albumins.

BACKGROUND: Cancer is a severe threat to the human society. In the scientific community worldwide cancer remains a big challenge as there are no remedies as of now. Cancer is quite complicated as it involves multiple signalling pathways and it may be caused by genetic disorders. Various natural products and synthetic molecules have been designed to prevent cell proliferation. Peptide-based anticancer drugs, however, are not explored properly. Though peptides have their inherent proteolytic instability, they could act as anticancer agents. RESULTS: In this present communication a suitably protected cystine based dipeptide and its deprotected form have been synthesized. Potent anticancer activities were confirmed by MTT assay (a laboratory test and a standard colorimetric assay, which measures changes in colour, for measuring cellular proliferation and phase contrast images. The IC50 value, a measure of the effectiveness of a compound in inhibiting biological or biochemical function, of these compounds ranges in the sub-micromolar level. The binding interactions with serum albumins (HSA and BSA) were performed with all these molecules and all of them show very strong binding at sub-micromolar concentration. CONCLUSIONS: This study suggested that the cystine-based dipeptides were potential anticancer agents. These peptides also showed very good binding with major carrier proteins of blood, the serum albumins. We are currently working on determining the detailed mechanism of anticancer activity of these molecules.

Melatonin inhibits matrix metalloproteinase-9 activity by binding to its active site.

The zinc-dependent matrix metalloproteinases (MMPs) are key enzymes associated with extracellular matrix (ECM) remodeling; they play critical roles under both physiological and pathological conditions. MMP-9 activity is linked to many pathological processes, including rheumatoid arthritis, atherosclerosis, gastric ulcer, tumor growth, and cancer metastasis. Specific inhibition of MMP-9 activity may be a promising target for therapy for diseases characterized by dysregulated ECM turnover. Potent MMP-9 inhibitors including an indole scaffold were recently reported in an X-ray crystallographic study. Herein, we addressed whether melatonin, a secretory product of pineal gland, has an inhibitory effect on MMP-9 function. Gelatin zymographic analysis showed a significant reduction in pro- and active MMP-9 activity in vitro in a dose- and time-dependent manner. In addition, a human gastric adenocarcinoma cell line (AGS) exhibited a reduced (~50%) MMP-9 expression when incubated with melatonin, supporting an inhibitory effect of melatonin on MMP-9. Atomic-level interaction between melatonin and MMP-9 was probed with computational chemistry tools. Melatonin docked into the active site cleft of MMP-9 and interacted with key catalytic site residues including the three histidines that form the coordination complex with the catalytic zinc as well as proline 421 and alanine 191. We hypothesize that under physiological conditions, tight binding of melatonin in the active site might be involved in reducing the catalytic activity of MMP-9. This finding could provide a novel approach to physical docking of biomolecules to the catalytic site of MMPs, which inhibits this protease, to arrest MMP-9-mediated inflammatory signals.