X=Y=ZH Systems as potential 1,3-dipoles. Part 58: Cycloaddition route to chiral conformationally constrained (R)-pro-(S)-pro peptidomimetics

Imines of (1S,9S)-t-butyl-9-amino-octahydro-6,10-dioxo-6H-pyridazino[1,2-a][1,2]diazepine-1-carboxylate undergo thermal (toluene, 110°C) or LiBr-DBU catalysed (MeCN, room temperature) regio- and stereo-specific cycloaddition to a range of chiral dipolarophiles giving enantiopure spiro-cycloadducts in excellent yield. The reactions proceed via intermediate NH azomethine ylides and litho azomethine ylides, respectively and results in the multiplication of chiral centres from 2 (one of which is lost in the process) to 5.     

Trihydroxy-2-thiaquinolizidine derivatives as a new class of bicyclic glycosidase inhibitors

Trihydroxy-2-thiaquinolizidines, a new class of bicyclic dideoxy-iminohexitol glycosidase inhibitor derivatives with nominally the d-gluco, l-ido, d-manno and l-gulo configurations were synthesized. X-ray analyses indicated that the preferred conformation for d-gluco and d-manno derivatives was a flat trans-fused system. Unlike deoxynojirimycin, the compound with d-gluco configuration was selective for α-glucosidases (yeast and rice) and showed no inhibitory activity towards β-glucosidase (almond), α-galactosidase (green coffee beans), α-galactosidase (E. coli) and α-mannosidase (jack bean), while the l-ido derivative was specific for β-glucosidase (almond).     

Cyclic voltammograms of iron and C-steels in oxalic acid solutions and investigation of the effect of phenyl phthalimide as corrosion inhibitors

Summary The electrochemical behaviour of Fe and C-steel samples in oxalic acid solutions was studied by the use of cyclic voltammetry. Two peaks were observed; the first one was the anodic peak and the second one an unexpected reductive dissolution peak which could be observed in the cathodic branch of cyclic voltammograms of all electrodes studied. The carbon content was found to increase the active dissolution of steels and to decrease their tendency towards passivation. The inhibitive efficiency of phenyl phthalimide derivatives on the active dissolution of Fe and steel samples in 0.1M oxalic acid were investigated.

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Cyclische Voltammogramme von Eisen und C-Stählen in Oxalsäurelösungen und der Einfluß von Phenylphthalimiden als Korrosionsinhibitoren

Zusammenfassung Das elektrochemische Verhalten von Eisen und C-Stählen in Oxalsäurelösungen wurde mit Hilfe cyclischer Voltammetrie studiert. Dabei treten zwei Signale auf: das anodische Signal sowie ein unerwartetes reduktives Lösungssignal. Letzteres wurde im kathodischen Zweig der cyclischen Voltammogramme aller untersuchten Elektroden gefunden. Der Kohlenstoffgehalt erhöht die aktive Auflösung von Stählen und erniedrigt ihre Tendenz zur Passivierung. Die Inhibitionseffizienz von Phenylphthalimiden für die aktive Auflösung von Eisen und Stahlproben in 0.1M Oxalsäure wurde untersucht.

     

Functionality map analysis of the active site cleft of human thrombin

Summary The Multiple Copy Simultaneous Search methodology has been used to construct functionality maps for an extended region of human thrombin, including the active site. This method allows the determination of energetically favorable positions and orientations for functional groups defined by the user on the three-dimensional surface of a protein. The positions of 10 functional group sites are compared with those of corresponding groups of four thrombin-inhibitor complexes. Many, but not all features, of known thrombin inhibitors are reproduced by the method. The results indicate that certain aspects of the binding modes of these inhibitors are not optimal. In addition, suggestions are made for improving binding by interaction with functional group sites on the thrombin surface that are not used by the thrombin inhibitors. Abbreviations: MCSS, multiple copy simultaneous search; PPACK, d-phenylalanyl-l-propyl-l-arginine chloromethane; NAPAP, N -(2-naphthylsulfonylglycyl)-d-para-amidinophenylalanylpiperidine; argatroban, (2R,4R)-4-methyl-1-[N -(3-methyl-1,2,3,4-tetrahydro-8-quinolinylsulfonyl)-l-arginyl]-2-piperidine carboxylic acid; rms, root mean square. The thrombin residues are numbered according to the chymotrypsin-based numbering by Bode et al. [8]. P1, P2, P3, etc., denote the peptide inhibitor residues on the amino-terminal side of the scissile peptide bond, and S1, S2, S3, etc., the corresponding subsites of thrombin     

Thiosemicarbazide-Substituted Coumarins as Selective Inhibitors of the Tumor Associated Human Carbonic Anhydrases IX and XII

A novel series of thiosemicarbazide-substituted coumarins was synthesized and the inhibitory effects against four physiologically relevant carbonic anhydrase isoforms I, II, IX and XII showed selective activities on the tumor-associated IX and XII isozymes. Molecular modeling studies on selected compounds 14a and 22a were performed. The binding modes of such compounds were determined assuming their enzymatically active structures (i.e., cinnamic acid) in the thermodynamically favored, and not previously explored, E geometry. Molecular modelling suggests multiple interactions within the enzymatic cavity and may explain the high potency and selectivity reported for the hCAs IX and XII.     

Insights on the Modulation of SIRT5 Activity: A Challenging Balance

SIRT5 is a member of the Sirtuin family, a class of deacetylating enzymes consisting of seven isoforms, involved in the regulation of several processes, including gene expression, metabolism, stress response, and aging. Considering that the anomalous activity of SIRT5 is linked to many pathological conditions, we present herein an overview of the most interesting modulators, with the aim of contributing to further development in this field.     

Design,Synthesis, Docking,DFT, MD Simulation Studies of a New Nicotinamide-Based Derivative: In Vitro Anticancer and VEGFR-2 Inhibitory Effects

A nicotinamide-based derivative was designed as an antiproliferative VEGFR-2 inhibitor with the key pharmacophoric features needed to interact with the VEGFR-2 catalytic pocket. The ability of the designed congener ((E)-N-(4-(1-(2-(4-benzamidobenzoyl)hydrazono)ethyl)phenyl)nicotinamide), compound 10, to bind with the VEGFR-2 enzyme was demonstrated by molecular docking studies. Furthermore, six various MD simulations studies established the excellent binding of compound 10 with VEGFR-2 over 100 ns, exhibiting optimum dynamics. MM-GBSA confirmed the proper binding with a total exact binding energy of −38.36 Kcal/Mol. MM-GBSA studies also revealed the crucial amino acids in the binding through the free binding energy decomposition and declared the interactions variation of compound 10 inside VEGFR-2 via the Protein–Ligand Interaction Profiler (PLIP). Being new, its molecular structure was optimized by DFT. The DFT studies also confirmed the binding mode of compound 10 with the VEGFR-2. ADMET (in silico) profiling indicated the examined compound’s acceptable range of drug-likeness. The designed compound was synthesized through the condensation of N-(4-(hydrazinecarbonyl)phenyl)benzamide with N-(4-acetylphenyl)nicotinamide, where the carbonyl group has been replaced by an imine group. The in-vitro studies were consonant with the obtained in silico results as compound 10 prohibited VEGFR-2 with an IC₅₀ value of 51 nM. Compound 10 also showed antiproliferative effects against MCF-7 and HCT 116 cancer cell lines with IC₅₀ values of 8.25 and 6.48 μM, revealing magnificent selectivity indexes of 12.89 and 16.41, respectively.     

Harnessing Protein-Ligand Interaction Fingerprints to Predict New Scaffolds of RIPK1 Inhibitors

Necroptosis has emerged as an exciting target in oncological, inflammatory, neurodegenerative, and autoimmune diseases, in addition to acute ischemic injuries. It is known to play a role in innate immune response, as well as in antiviral cellular response. Here we devised a concerted in silico and experimental framework to identify novel RIPK1 inhibitors, a key necroptosis factor. We propose the first in silico model for the prediction of new RIPK1 inhibitor scaffolds by combining docking and machine learning methodologies. Through the data analysis of patterns in docking results, we derived two rules, where rule #1 consisted of a four-residue signature filter, and rule #2 consisted of a six-residue similarity filter based on docking calculations. These were used in consensus with a machine learning QSAR model from data collated from ChEMBL, the literature, in patents, and from PubChem data. The models allowed for good prediction of actives of >90, 92, and 96.4% precision, respectively. As a proof-of-concept, we selected 50 compounds from the ChemBridge database, using a consensus of both molecular docking and machine learning methods, and tested them in a phenotypic necroptosis assay and a biochemical RIPK1 inhibition assay. A total of 7 of the 47 tested compounds demonstrated around 20–25% inhibition of RIPK1’s kinase activity but, more importantly, these compounds were discovered to occupy new areas of chemical space. Although no strong actives were found, they could be candidates for further optimization, particularly because they have new scaffolds. In conclusion, this screening method may prove valuable for future screening efforts as it allows for the exploration of new areas of the chemical space in a very fast and inexpensive manner, therefore providing efficient starting points amenable to further hit-optimization campaigns.     

Methods to Study Naphthenate Formation in w/o Emulsions by the Use of a Tetraacid Model Compound

Precipitation of naphthenate salts is normally a problem in the processing of acidic crude oils. In this study, the goal was to find suitable methods to investigate the interfacial reaction between tetraacid and calcium under emulsified conditions. Two different systems have been studied depending on composition and applied shear. The influence of inhibitors has been investigated and the same inhibitor was found to be the most effective one regardless of the system. Depletion of tetraacid in the oil phase was analyzed with UV-vis and HPLC. Interfacial area and droplet size in the emulsions were measured with fluorescence microscope and pulse-field gradient NMR. Since this reaction takes place over the interface, the investigation clearly documents, the importance of the total interfacial area of the emulsified system.