Spirulina platensis – A novel green inhibitor for acid corrosion of mild steel

The inhibition of the corrosion of mild steel in 1 M HCl and 1 M H₂SO₄ by Spirulina platensis has been studied at different temperatures viz., 303 K, 313 K and 323 K by weight loss method, potentiodynamic polarization method, electrochemical impedance spectroscopy measurements and SEM analysis. The inhibition efficiency increased with increasing concentration of the inhibitor in both HCl and H₂SO₄ media. The results of weight loss studies correlated well with those of impedance and polarization studies. From the results of weight loss studies at various temperatures, the mode of adsorption is confirmed to be physisorption. Further the adsorption has been found to follow Temkin isotherm. From this isotherm, the free energy of adsorption (ΔG) and entropy (ΔS) are calculated. The study reveals the corrosion inhibition potential of S. platensis in both the acid media, thus bringing to light another facet of this microalga as it has so far been used only to produce antioxidant principles, finding extensive use in medicine especially as neutraceutical.     

Computational insights about the dynamic behavior for the inclusion process of deprotonated and neutral aspirin in β-cyclodextrin

A high-efficiency microwave irradiation (MW) assisted protocol was proposed to synthesize series SPE-β-CD with specific degree of substitution (DS) in the sodium hydroxide solution. This protocol provided an eco-friendly way to modify the cyclodextrins with bulky sulfopropyl substituent on the purpose of avoiding organic solvents and high quantities of thermal energy. Temperature and energy distribution became more uniform under the new method accordingly. Therefore, not only the reaction time reduced significantly from over 20 h to a few hours, but also the DS increased up according to ¹H NMR spectroscopy, MS and elemental analysis results. Most importantly, the effects of reaction parameters on DS were compared both under MW method and conventional heating method, and were sufficiently studied to guarantee the aforementioned results could be better reproduced and DS of products could become more specific through the synthesis process. Products structures were characterized by FT-IR, DSC, and ¹³C NMR spectroscopy.     

Multi-targeted directed ligands for Alzheimer’s disease: design of novel lead coumarin conjugates

Alzheimer’s Disease (AD) is a neurodegenerative disease characterized by central nervous system insults with progressive cognitive (memory, attention) and non-cognitive (anxiety, depression) impairments. Pathophysiological events affect predominantly cholinergic neuronal loss and dysfunctions of the dopaminergic system. The aim of the current study was to design multi-targeted directed lead structures based on the coumarin scaffold with inhibitory properties at two key enzymes in disease relevant systems, i.e. acetylcholinesterase (AChE) and monoamine oxidase B (MAO-B). Conventional and microwave synthetic methods were utilized to synthesize coumarin scaffold-based novel morpholino, piperidino, thiophene and erucic acid conjugates. Biological assays indicated that the coumarin–morpholine ether conjugate BPR 10 was the most potent hMAO-B inhibitor. The coumarin–piperidine conjugates BPR 13 and BPR 12 were the most potent inhibitors of eeAChE at 100 μM and 1 μM, respectively. Molecular modelling studies were conducted with Accelrys^® Discovery Studio^® V3.1.1 utilising the published hMAO-B (2V61) and hAChE (4EY7) crystal structures. Compound BPR 10 occupies both the entrance and substrate cavities of the active site of MAO-B. BPR 13 resides in both the peripheral anionic site (PAS) and the catalytic anionic site (CAS) of hAChE. This study demonstrated that the coumarin scaffold serves as a promising pharmacophore for MTDLs design.     

A novel concept for the improvement of the Ni–Mo/Al2O3-based nanocatalyst system: design and analysis

A new Ni?CMo/Al₂O₃-based nano catalyst composition was developed and manufactured by a proprietary catalyst preparation technology for diesel hydrotreatment. The nanocatalyst has been performing commercially since September 2011, consistently producing ultra low-sulfur diesel of Euro-IV/V standards from a feedstock containing 1.75?wt% sulfur. In addition to lowering sulfur content, the catalyst also enhances cetane number and reduces boiling end-point to obtain diesel with better quality. The nanocatalyst was characterized by X-ray photoelectron spectroscopy to ascertain the electronic state of metal species. The morphological characterization of the nanocatalyst carried out by TEM revealed the presence of nano-sized MoS₂ slab structures. The performance of the nanocatalyst is mainly attributed to MoS₂ slabs with increased stacking which in turn are generated from the customized metal-sulfide precursors.     

Advances and trends in the design, analysis, and characterization of polymer–protein conjugates for “PEGylaided” bioprocesses

In addition to their use as therapeutics and because of their enhanced properties, PEGylated proteins have potential application in fields such as bioprocessing. However, the use of PEGylated conjugates to improve the performance of bioprocess has not been widely explored. This limited additional industrial use of PEG-protein conjugates can be attributed to the fact that PEGylation reactions, separation of the products, and final characterization of the structure and activity of the resulting species are not trivial tasks. The development of bioprocessing operations based on PEGylated proteins relies heavily in the use of analytical tools that must sometimes be adapted from the strategies used in pharmaceutical conjugate development. For instance, to evaluate conjugate performance in bioprocessing operations, both chromatographic and non-chromatographic steps must be used to separate and quantify the resulting reaction species. Characterization of the conjugates by mass spectrometry, circular dichroism, and specific activity assays, among other adapted techniques, is then required to evaluate the feasibility of using the conjugates in any operation. Correct selection of the technical and analytical methods in each of the steps from design of the PEGylation reaction to its final engineering application will ensure success in implementing a "PEGylaided" process. In this context, the objective of this review is to describe technological and analytical trends in developing successful applications of PEGylated conjugates in bioprocesses and to describe potential fields in which these proteins can be exploited.     

Hydroxypyridinones as “privileged” chelating structures for the design of medicinal drugs

Hydroxypyridinones (HPs) are a family of N-heterocyclic core chelators which, based on their specific metal-coordination, easy manipulation/derivatization and biocompatibility, have been an attractive target for the development of new pharmaceutical drugs with manifold uses. Herein we describe the most recent advances reported in the literature on HPs, with a special focus on the metal chelating properties of the 3-hydroxy-4-pyridinone (3,4-HP) derivatives, and the different approaches used to functionalize these chelators to improve their biological properties, namely in terms of bioavailability and specific bio-targeting abilities. Representative examples of HPs are included, mostly for applications as chelating drugs for sequestration or passivation of metal overload or deregulated biometals, but also as metallodrugs for potential diagnostic/therapeutic purposes. These examples are discussed in terms of the chelating properties and structure–activity relationships.     

A deep learning “ticket” for single-molecule analysis of protein stoichiometry

<正>Proteins are the fundamental of life activities, and they participate in a myriad of physiological processes including signal transduction, ion transport and immune response.Notably, the aggregation states of proteins are dynamically changed in these physiological processes, such as undergoing ligand-induced monomer to dimer, or dimer to oligomer. As such, stoichiometric analysis of protein oligomerization state is highly important for elucidating structure-function relationship of proteins, pathological regulation mechanism and drug development [1]. Single-     

Molecular dynamics and high throughput binding free energy calculation of anti-actin anticancer drugs—New insights for better design

Actin cytoskeleton plays an important role in cancerous cell progression. Till date many anticancer toxins are discovered that binds to different sites of actin. Mechanism of action of these toxins varies with respect to the site where they bind to actin. Latrunculin A (LAT) binds closely to nucleotide binding site and Reidispongiolide binds to the barbed end of actin. LAT is reported to reduce the displacement of domain 2 with respect to domain 1 and allosterically modulate nucleotide exchange. On the other hand Reidispongiolide binds with the higher affinity to actin and competes with the DNaseI binding loop once the inter-monomer interaction has been formed. Evolving better actin binders being the aim of this study we conducted a comparative molecular dynamics of these two actin-drug complexes and actin complexed with ATP alone, 50 ns each. High throughput binding free energy calculations in conjugation with the high-throughput MD simulations was used to predict modifications in these two renowned anti-actin anticancer drugs for better design. Per residue energy profiling that contribute to free energy of binding shows that there is an unfavourable energy at the site where Asp157 interacts with 2-thiazolidinone moiety of LAT. Similarly, unfavourable energies are reported near macrocyclic region of Reidispongiolide specifically near carbons 7, 11 & 25 and tail region carbons 27 & 30. These predicted sites can be used for modifications and few of these are discussed in this work based on the interactions with the binding site residues. The study reveals specific interactions that are involved in the allosteric modulation of ATP by these two compounds. Glu207 closely interacting with LAT A initiates the allosteric effect on ATP binding site specifically affecting residues Asp184, Lys215 and Lys336. RGA bound actin shows high anti-correlated motions between sub domain 3 and 4. Unlike LAT A, Reidispongiolide induces a flat structure of actin which definitely should affect actin polymerisation and lead to disassembly of actin filaments.     

Computational insight into protein circular dichroism: detailed analysis of contributions of individual chromophores in TEM-1 ��-lactamase

Circular dichroism (CD) is an extremely powerful method in dynamically developed areas such as proteomics and drug design. However, it is characterized with a low signal resolution, and therefore it is difficult to assign the signals to specific chromophores. In this study, we demonstrate a systematic computational strategy for revealing the contributions of all individual chromophores to complex near-UV CD spectra of proteins. The methodology not only reveals the individual chromophores contributions without any structural perturbation, but also makes mechanistic insight into physical mechanisms possible. We have applied our strategy to a TEM-1 ??-lactamase from E. coli??an enzyme of crucial importance to bacterial resistance to ??-lactam antibiotics. We analyzed the free enzyme structure, two acyl-enzyme structures and the structure of the transition state analog, thus simulating delicate but very important conformational changes that could take place during enzyme catalysis and binding. Such analysis also accounts for the important effects of the electrostatic environment that could be altered during experiments. We revealed in silico (without structural manipulations) that the strongest contribution in the near-UV CD is due to W210. The individual contribution of each aromatic chromophore was very dynamic with respect to structural changes and electrostatic effects. In contrast, the disulfide group contribution is relatively resistant to such structural dynamics but was dramatically influenced by alterations in the electrostatic environment.     

Discovery of new inhibitor for the protein arginine deiminase type 4 (PAD4) by rational design of α-enolase-derived peptides

Rheumatoid arthritis (RA) is an inflammatory autoimmune disease affecting about 0.24 % of the world population. Protein arginine deiminase type 4 (PAD4) is believed to be responsible for the occurrence of RA by catalyzing citrullination of proteins. The citrullinated proteins act as autoantigens by stimulating an immune response. Citrullinated α-enolase has been identified as one of the autoantigens for RA. Hence, α-enolase serves as a suitable template for design of potential peptide inhibitors against PAD4. The binding affinity of α-enolase-derived peptides and PAD4 was virtually determined using PatchDock and HADDOCK docking programs. Synthesis of the designed peptides was performed using a solid phase peptide synthesis method. The inhibitory potential of each peptide was determined experimentally by PAD4 inhibition assay and IC₅₀ measurement. PAD4 assay data show that the N-P2 peptide is the most favourable substrate among all peptides. Further modification of N-P2 by changing the Arg residue to canavanine [P2 (Cav)] rendered it an inhibitor against PAD4 by reducing the PAD4 activity to 35 % with IC₅₀ 1.39 mM. We conclude that P2 (Cav) is a potential inhibitor against PAD4 and can serve as a starting point for the development of even more potent inhibitors.     

A novel synthetic use of 2-bromo- 1-methylpyridinium iodide for macrolactamization

Using 2-bromo-1-methylpyridimium iodide as carboxyl activating agent, 10 ansa-macrolactams were prepared conveniently from the corresponding seco-precursor w-aminoacids in the yields of 78-2%.     

Tomocomd-Cardd, a novel approach for computer-aided ‘ rational’ drug design: I. Theoretical and experimental assessment of a promising method for computational screening and in silico design of new anthelmintic compounds

Summary In this work, the TOMOCOMD-CARDD approach has been applied to estimate the anthelmintic activity. Total and local (both atom and atom-type) quadratic indices and linear discriminant analysis were used to obtain a quantitative model that discriminates between anthelmintic and non-anthelmintic drug-like compounds. The obtained model correctly classified 90.37% of compounds in the training set. External validation processes to assess the robustness and predictive power of the obtained model were carried out. The QSAR model correctly classified 88.18% of compounds in this external prediction set. A second model was performed to outline some conclusions about the possible modes of action of anthelmintic drugs. This model permits the correct classification of 94.52% of compounds in the training set, and 80.00% of good global classification in the external prediction set. After that, the developed model was used in virtual in silicoscreening and several compounds from the Merck Index, Negwers handbook and Goodman and Gilman were identified by models as anthelmintic. Finally, the experimental assay of one organic chemical (G-1) by an in vivo test coincides fairly well (100) with model predictions. These results suggest that the proposed method will be a good tool for studying the biological properties of drug candidates during the early state of the drug-development process.     

Development and analysis of a novel AF11–2 aptamer capable of enhancing the fluorescence of aflatoxin B1

Aflatoxin B1 (AFB1) is one of the most common mycotoxins that threatens human health. As single-stranded oligonucleotides with high affinity and specificity, aptamers have incomparable effect on the targeted detection of AFB1. Herein, after 11 rounds of selection and analysis using a modified affinity chromatography-based SELEX strategy, the truncated 37 nt aptamer AF11–2 was successfully obtained. The aptamer shows good detection performance for AFB1, and can sensitively detect AFB1 in the range of 100–1000 nmol/L, with a detection limit of 42 nmol/L. In the detection of pretreated edible peanut oil samples, AF11–2 aptamer also showed a high recovery rate and good stability for AFB1, and achieved satisfactory results. In addition, AF11–2 aptamer can significantly enhance the fluorescence ability of AFB1, which is not available in traditional Afla17–2–3 aptamer. After molecular docking analysis, it was found that AF11–2 and Afla17–2–3 had different nucleotide binding sites for AFB1. Afla17–2–3 binds to the carbonyl O of AFB1, while AF11–2 binds to the pyrrolic O of AFB1, which may be the main reason that AF11–2 can enhance the fluorescence of AFB1.     

Computational design of new organic (D–π–A) dyes based on benzothiadiazole for photovoltaic applications,especially dye-sensitized solar cells

Research on Chemical Intermediates - A theoretical study on four organic dyes based on bis(4-hexyloxy)triphenylamine as donor and electron acceptor cyanoacrylic acid with a...     

A novel colorimetric and “turn-on” fluorescent sensor for selective detection of Cu2+

In this work, a new highly selective and sensitive fluorescent sensor for detecting Cu²⁺ was developed based on rhodamine fluorophore. It displayed strong fluorescence “turn-on” effect upon addition of Cu²⁺, and possessed the function of naked eye recognition. The fluorescence enhancement also enabled the sensor to quantitatively analyze Cu²⁺ due to the formation of a stable 1:1 metal–ligand complex in a short time, and the complex possesses relatively good pH stability. In addition, the density functional theory calculations were adopted to investigate the molecular orbitals as well as the spatial structure. Simultaneously, the cell imaging and zebra fish experiments provided a broader application prospect in biological system.