Phosphoprotein Analysis by MALDI-TOF Mass Spectrometry using On-Probe Tandem Proteolysis and Dephosphorylation

In this investigation, methods based on on-probe enzymatic cleavage matrix-assisted laser desorption/ionization time-of-flight mass spectrometric (MALDI-TOF-MS) analyses have been developed, allowing the rapid assignment of phosphorylation sites within phosphoproteins. The procedures involved robotic sample deposition of a phosphoprotein, such as intact bovine β-casein, on stainless steel or gold MALDI plates, on-probe proteolysis with trypsin for 10–180?s at 37°C, on-probe dephosphorylation for 1–10?min at 37°C with alkaline phosphatase, followed by differential mass spectrometry with peptide mass mapping. The dephosphorylation conditions were initially optimized using in-solution tryptic digestion of the phosphoprotein performed in the presence of MS-compatible anionic surfactant sodium 3-[(2-methyl-2-undecyl-1,3-dioxolan-4-yl)methoxy]-1-propanesulfonate. Two methods of trypsin deactivation were investigated, cooling and quenching by acidification, which resulted in the surfactant either staying intact or becoming cleaved, respectively. Since the surfactant had no detrimental effects on dephosphorylation of phosphopeptides, the acidification and neutralization steps were not included in the final analytical method. A protocol, comprising on-probe tandem, surfactant-aided proteolysis for 3?min followed by on-probe dephosphorylation for 10?min was thus established, allowing the rapid identification of location and sequence of phosphopeptides within a phosphoprotein by these procedures.     

Design and synthesis of a Cu(II)-complex-based carbazole-hemicyanine hybrid for fluorescent sensing of H2S in SDS micellar solution

A novel fluorescent chemosensor HACBA with carbazole-hemicyanine fluorophore as signal reporter and N,N,N'-tri(2-pyridylmethyl)ethylenediamine (TPEA) as binding sites was designed and synthesized. Its assemblies with anionic surfactant sodium dodecyl sulfate (SDS) show improved fluorescence emission stability and enhanced fluorescence intensity. HACBA/SDS system can selectively recognize Cu²⁺, which led to a dramatic fluorescence quenching. The in situ resultant HACBA-Cu(II)/SDS ensemble functioned as a highly selective and sensitive sensor for H₂S with a turn-on fluorescent response. Our results show that the “on-off-on” molecular switch occured through the reversible formation-dissociation reaction between HACBA-Cu(II) complex and HACBA/CuS in the SDS micellar solution, and at least 3 cycles of on-off-on switches were observed.     

Greener approach: Ionic liquid [Et3NH][HSO4]-catalyzed multicomponent synthesis of 4-arylidene-2-phenyl-5(4H)oxazolones under solvent-free condition

We have developed simple, greener, safer multicomponent synthesis series of 4-arylidene-2-phenyl-5(4H) oxazolones 4(a-r) catalyzed by Bronsted acid ionic liquid as triethylammonium hydrogen sulfate [Et₃NH][HSO₄] and catalytic amount of acetic anhydride and sodium acetate with excellent yields (90–99%). The protocol offers economical, environmentally benign, solvent-free conditions, and recycle–reuse of the catalyst and easily available starting as benzoyl chloride 1, amino acid 2 and a variety of aldehydes 3. The cyclization followed by condensation of benzoyl chloride, amino acid, and a variety of aldehydes catalyzed by ILs [Et₃NH][HSO₄] and catalytic amount of acetic anhydride and sodium acetate. The final products were confirmed by their characterization data such as FTIR, ¹H-NMR, ¹³C-NMR, Mass, high-resolution mass spectra and were compared with its reported method.     

Efficient copper-catalyzed Sonogashira coupling reactions and simulation studies

A practical copper-catalyzed I-substitutions of alkyl-2-iodobenzoates with alkynes have been developed using Cu powder as a catalyst under solvent, cocatalyst, and base-free conditions. This reaction system is new, facile, efficient, and economical that gives Sonogashira coupling products in excellent yields (up to 97%). The coupled products (A–J) were characterized by CHNS, ¹H NMR, and ¹³C NMR and are found soluble in ethyl acetate and dichloromethane. In addition, simulation studies of A–J were performed with aspulvinone dimethylallyltransferase enzyme and observe good binding affinity. The reported compounds may act as anti-cizmatics, anti-fobic in future and also have the inhibition of aspulvinone dimethylallyltransferase properties to control Alzheimer’s, Schizophrenia, etc. diseases.     

Facile synthesis of novel dihydroquinoline-3,3-dicarbonitriles in the presence of glacial acetic acid as a catalyst under solvent-free conditions

A series of novel dihydroquinoline derivatives were synthesized using malononitrile, 2-aminobenzoic acid, and benzaldehydes in the presence of a catalytic amount of acetic acid, without the use of any additional cocatalyst, under solvent-free conditions. The reaction is characterized by high efficiency, easy workup, simple purification of the products, and availability of catalyst.     

Solvent-free synthesis of dibenzo[b,j][1,10]phenanthroline derivatives using Eaton’s reagent as catalyst

A new class of dibenzo[b,j][1,10]phenanthrolines has been prepared. The synthon acridones were achieved in very good yield by a one-pot reaction of 2-amino-5-chloro or 2′-chloro/flouro-substituted benzophenones with 1,2-cyclohexanedione in the presence of freshly prepared Eaton’s reagent (phosphorus pentoxide–methanesulfonic acid) without solvent, through Friedländer synthesis. Then these intermediates were reacted with 2-amino-3,5-dibromobenzaldehyde to afford 1,3-dibromo-10-chloro-8-aryl-6,7-dihydrodibenzo[b,j][1,10]phenanthroline. Also an one-pot reaction between 2?mol of 2-amino-5-chloro aryl benzophenones with 1?mol of 1,2-cyclohexanedione to get 3,10-dichloro-5,8-diaryl-6,7-dihydrodibenzo[b,j][1,10]phenanthroline has also been reported. The newly synthesized structures of the compounds were deduced by spectroscopic techniques.     

Synthesis of 2,3,6-trisubstituted pyridines by transition-metal free cyclization of 1,3-diynes with amino acids

Amino acids are firstly employed in transition-metal free heterocyclization reaction of 1,3-diynes in the presence of K₃PO₄ and DMSO at 120 °C. This method produces 2,3,6-trisubstituted pyridines with up to 86% yield. The –CO₂H group on the amino acids is crucial for this heterocyclization reaction. The mechanism of such a heterocyclization reaction is discussed, as well.     

Adaptive‐numerical‐bias metadynamics

A metadynamics scheme is presented in which the free energy surface is filled with progressively adding adaptive biasing potentials, obtained from the accumulated probability distribution of the collective variables. Instead of adding Gaussians with assigned height and width in conventional metadynamics method, here we add a more realistic adaptive biasing potential to the Hamiltonian of the system. The shape of the adaptive biasing potential is adjusted on the fly by sampling over the visited states. As the top of the barrier is approached, the biasing potentials become wider. This decreases the problem of trapping the system in the niches, introduced by the addition of Gaussians of fixed height in metadynamics. Our results for the free energy profiles of three test systems show that this method is more accurate and converges more quickly than the conventional metadynamics, and is quite comparable (in accuracy and convergence rate) with the well‐tempered metadynamics method. © 2017 Wiley Periodicals, Inc.     

Tinker‐OpenMM: Absolute and relative alchemical free energies using AMOEBA on GPUs

The capabilities of the polarizable force fields for alchemical free energy calculations have been limited by the high computational cost and complexity of the underlying potential energy functions. In this work, we present a GPU‐based general alchemical free energy simulation platform for polarizable potential AMOEBA. Tinker‐OpenMM, the OpenMM implementation of the AMOEBA simulation engine has been modified to enable both absolute and relative alchemical simulations on GPUs, which leads to a ∼200‐fold improvement in simulation speed over a single CPU core. We show that free energy values calculated using this platform agree with the results of Tinker simulations for the hydration of organic compounds and binding of host–guest systems within the statistical errors. In addition to absolute binding, we designed a relative alchemical approach for computing relative binding affinities of ligands to the same host, where a special path was applied to avoid numerical instability due to polarization between the different ligands that bind to the same site. This scheme is general and does not require ligands to have similar scaffolds. We show that relative hydration and binding free energy calculated using this approach match those computed from the absolute free energy approach. © 2017 Wiley Periodicals, Inc.     

Steady-state fluorescence investigations of aqueous binary mixtures of myristyl alcohol based bis-sulfosuccinate anionic gemini surfactant and effect of different conventional surfactants therein

The present research work is associated with the fluorescence investigations of binary aqueous mixed surfactants solutions of anionic bis-sulfosuccinate gemini surfactant (BSGSMA_1,8) and three different conventional surfactants—anionic viz. sodium dodecyl sulfate (SDS), cationic viz. cetyl trimethyl ammonium bromide (CTAB), and nonionic surfactant viz. Triton X 100. Steady-state fluorescence spectroscopy technique has been utilized to examine the micellization behavior of aqueous solution of pure myristyl alcohol-based BSGSMA_1,8 having flexible methylene chain [(CH₂)₈] as spacer group. Critical micelle concentration (CMC), aggregation number (N), and micropolarity of pure and mixed surfactants systems were explored during the investigations. The results revealed the best synergism behavior of prepared gemini BSGSMA_1,8 with SDS as compared to CTAB and Triton X 100. The maximum reduction in the value of pyrene intensity ratio (I₁/I₃) was observed for gemini and SDS mixed surfactant solution. On the other hand, the increased I₁/I₃ value of mixed gemini with Triton X 100 exhibited that mixed surfactant system of anionic gemini BSGSMA_1,8 with non-ionic Triton X 100 is not as compact as other mixed surfactant systems. Aggregation number increased and micropolarity decreased with increased concentration of gemini surfactants.