Inhibition of Insulin-Regulated Aminopeptidase (IRAP) by Arylsulfonamides

The inhibition of insulin-regulated aminopeptidase (IRAP, EC 3.4.11.3) by angiotenesin IV is known to improve memory and learning in rats. Screening 10 500 low-molecular-weight compounds in an enzyme inhibition assay with IRAP from Chinese Hamster Ovary (CHO) cells provided an arylsulfonamide (N-(3-(1H-tetrazol-5-yl)phenyl)-4-bromo-5-chlorothiophene-2-sulfonamide), comprising a tetrazole in the meta position of the aromatic ring, as a hit. Analogues of this hit were synthesized, and their inhibitory capacities were determined. A small structure–activity relationship study revealed that the sulfonamide function and the tetrazole ring are crucial for IRAP inhibition. The inhibitors exhibited a moderate inhibitory potency with an IC₅₀=1.1±0.5 μm for the best inhibitor in the series. Further optimization of this new class of IRAP inhibitors is required to make them attractive as research tools and as potential cognitive enhancers.     

Monte Carlo method based QSAR modelling of natural lipase inhibitors using hybrid optimal descriptors

Obesity is one of the most provoking health burdens in the developed countries. One of the strategies to prevent obesity is the inhibition of pancreatic lipase enzyme. The aim of this study was to build QSAR models for natural lipase inhibitors by using the Monte Carlo method. The molecular structures were represented by the simplified molecular input line entry system (SMILES) notation and molecular graphs. Three sets – training, calibration and test set of three splits – were examined and validated. Statistical quality of all the described models was very good. The best QSAR model showed the following statistical parameters: r² = 0.864 and Q² = 0.836 for the test set and r² = 0.824 and Q² = 0.819 for the validation set. Structural attributes for increasing and decreasing the activity (expressed as pIC₅₀) were also defined. Using defined structural attributes, the design of new potential lipase inhibitors is also presented. Additionally, a molecular docking study was performed for the determination of binding modes of designed molecules.     

Prediction for understanding the effectiveness of antiviral peptides

The low efficacy of current antivirals in conjunction with the resistance of viruses against existing antiviral drugs has resulted in the demand for the development of novel antiviral agents. Antiviral peptides (AVPs) are those bioactive peptides having virucidal activity and they can be developed into promising antiviral drugs. They are shorter length peptides having the ability to cease the progression of viral infections. The use of antiviral peptides in therapeutics has recently attracted the attention of the research community. The development and identification of AVPs is imperative for the discovery of novel therapeutics for viral infections. In the present work, a meta classifier (stacking) based approach is implemented for the prediction of IC₅₀ (half maximal inhibitory concentration) and pIC₅₀ (negative log of half maximal inhibitory concentration) values. The best prediction model with evolutionary information and local alignment scores as features achieved a correlation coefficient values of 0.670 and 0.753 on the training and testing sets respectively for IC₅₀. Further, the prediction of pIC₅₀ reached a correlation coefficient value of 0.797 and 0.789 for training and testing sets respectively. For the development of machine learning models involved in the prediction of IC₅₀, the use of pIC₅₀ over IC₅₀ is recommended as the target variable. Further on a systematic comparison of AVPs with high IC₅₀ values and Low IC₅₀ values, it is revealed that higher mean charge and tiny amino acids are preferred and higher length and consecutive hydrophilic amino acids are avoided in the former.     

Investigation of indirubin derivatives: a combination of 3D-QSAR,molecular docking,and ADMET towards the design of new DRAK2 inhibitors

Kinase-related apoptosis-inducing kinase 2 (DRAK2) is a serine/threonine kinase and belongs to the death-associated protein kinase DPAK family, which is responsible for induction of apoptosis in many cell types. Thus, DRAK2 is regarded as a promising target for treatment of autoimmune diseases. To investigate the binding between DRAK2 and indirubin inhibitors and design potent inhibitors, a three-dimensional quantitative structure-activity relationship (3D-QSAR) and molecular docking were performed. Comparative Molecular Similarity Indices Analysis (CoMSIA) was developed using 33 molecules having pIC₅₀ ranging from 8.523 to 5.000 (IC₅₀ in nM). The best CoMSIA model gave a significant coefficient of determination (R²?=?0.93), as well as a (leave-one-out cross-validation coefficient Q² of 0.81. The predictive ability of this model was evaluated by external validation using a test set of eight compounds and yielded a predicted coefficient of determination R²_test of 0.94. The contour maps could provide structural features to improve inhibitory activity. Good consistency between contour maps and molecular docking strongly suggests that the molecular modeling is reliable. Based on these satisfactory results, we designed several new DRAK2 inhibitors and their inhibitory activities were predicted using different models, which are developed on different training and test sets. Additionally, these newly designed inhibitors showed promising results in the preliminary in silico ADMET evaluations compared to the best inhibitor from the studied dataset. This study could be useful in lead identification and optimization for early drug discovery of DRAK2 inhibitors.     

Prediction of different antibacterial activity in a new set of formyl hydroxyamino derivatives with potent action on peptide deformylase using structural information

Due to the essential role of peptide deformylase (PDF) at the bacterial growth cycle, it is a noteworthy target for developing a novel antibacterial agent. In the current study, the antibacterial activities of a set of 44 new structures of formyl hydroxyamino derivatives as PDF inhibitors were quantified using quantitative structure–activity relationship (QSAR). Artificial neural networks (ANN) were used as a chemometrics tool for QSAR modeling. Three quantitative models were suggested to relate the chemical structural features of the formyl hydroxyamino derivatives to their antibacterial activities (pIC₅₀) against Staphylococcus aureus, methicillin-susceptible S. aureus (MSSA), and methicillin-resistant S. aureus (MRSA) peptide deformylase. The sufficiency of the model for prediction of the antibacterial activities of the desired PDF inhibitor compounds against S. aureus, MSSA, and MRSA was statistically demonstrated according to the validation parameters such as coefficient of determination (R²), mean square error (MSE) in training, validation, and prediction sets, and also using applicability domain (AD) and randomization test.

     

Discovery of a novel serine protease inhibitor utilizing a structure-based and experimental selection of fragments technique

We report a set of strategies to develop novel ligands (Structure Based and Experimental Selection of Fragments: SbE-SF). First, a docking simulation utilizing DOCK3.5 is performed in order to screen the fragment database, which was generated with the in-house program FRAGMENT++ specifically for docking simulation purposes. Although the affinity of these small molecules (fragments) is expected to be low, the affinity of fragments selected by computation is assayed by experiment to determine which ones can be potent inhibitors. After determining such key fragments, additional fragments are attached to the key ones in order to increase the binding affinity,taking into account the binding modes predicted by computation. This method has been applied to a thrombin inhibitor study, resulting in the discovery of a novel inhibitor exhibiting pIC₅₀ = 7.9.     

Design,Synthesis and Evaluation of Substituted N-(3-Arylpropyl)-9,10-dihydro-9-oxoacridine-4-carboxamides as Potent MDR Reversal Agents in Cancer

A novel class of molecules with structure N‐(3‐arylpropyl)‐9,10‐dihydro‐9‐oxoacridine‐4‐carboxamides ( 20 – 29 ) were designed by generating a pharmacophore for potent MDR reversal activity using phase drug design software. The designed molecules were synthesized by a novel synthesis route and evaluated for their inhibitory effects on the transport activity of P‐glycoprotein (P‐gp) by standard Hoechst 33342 assay method. Based on the pIC₅₀ values of ten title compounds screened, three compounds exhibited better activity as compared to Verapamil used as standard.     

Room-Temperature-Observable Interconversion Between Si(IV) and Si(II) via Reversible Intramolecular Insertion Into an Aromatic C−C Bond

An easily isolable silacycloheptatriene (silepin) 1 b was synthesized from the reaction of a N-heterocyclic imino (IPrN) substituted tribromosilane IPrNSiBr₃ with the sterically congested bis(trimethylsilyl)triisopropylsilyl silanide KSi(TMS)₂Si(ⁱPr)₃ (BTTPS). In solution, the Si(IV) silepin 1 b is in a thermodynamic equilibrium with the acyclic Si(II) silylene 1 a . The relative concentration of the Si(II) or Si(IV) isomers can be controlled by temperature variation and observed by variable temperature NMR and UV/Vis spectroscopy. DFT calculations show a small reaction barrier for the Si(II)⇌Si(IV) interconversion and a small energy gap between the Si(II) and Si(IV) species. The reactivity of 1 a/b is demonstrated on a variety of small molecules.     

Irreversible enzyme inhibitors. LXXXIII. Candidate active-site-directed irreversible inhibitors of dihydrofolic reductase. VIII. Derivatives of 2,4-diaminopyrimidine. II

2,4-Diamino-6-(p-aminophenethyl)pyrimidines with a 5-phenylbutyl (XIX) and 5-(p-chlorophenyl) (VIII) substituent were synthesized by condensation of the corresponding pyrimidine-6-carboxaldehydes (XVI, X) with the Wittig reagent derived from p-nitro-benzyl bromide, followed by catalytic hydrogenation. Selective bromoacetylation of VIII and XIX afforded the candidate active-site-directed irreversible inhibitors of dihydrofolic reductase, namely, 6-(p-bromoacetamidophenethyl)-2,4-diaminopyrimidine with a 5-(p-chlorophenyl)- (IV) and 5-phenylbutyl- (III) substituents. Although III and IV were excellent reversible inhibitors of dihydrofolic reductase, neither showed any inactivation of the enzyme; in contrast, the corresponding 2-amino-6-(p-bromoacetamidophenethyl)-5-phenylbutyl-4-pyrimidinol (II) - which differs from III only in the 4-substituent (NH₂ vs. OH) - was an excellent active-site-directed irreversible inhibitor of dihydrofolic reductase, but II was a poor reversible inhibitor. Thus the conformations of II and III are most probably different when complexed to dihydrofolic reductase.     

The identification of new ATAD2 bromodomain inhibitors: the application of combined ligand and structure-based virtual screening

Ligand-based virtual screening (LBVS) and structure-based virtual screening (SBVS) approaches were used to identify new inhibitors for ATAD2 bromodomain. The LBVS approach was used to search 23,129,083 clean compounds to identify compounds similar to an active compound with reported pIC₅₀ equal to 7.2. Based on LBVS results, 19 compounds were selected. To perform SBVS, by applying nine filters on 23,129,083 clean compounds, 1,057,060 compounds were selected. After performing SBVS on these selected compounds with idock software, 16 compounds with the lowest binding energies were selected. More accurate molecular docking analysis was performed on these 35 selected compounds by using iGEMDOCK software and six of them with the lowest binding energies were selected as hit compounds. These compounds were zinc36647229, zinc77969074, zinc13637358, zinc77971540, zinc12991296 and zinc19374204.     

Inhibitors of the Bifunctional 2‐C‐Methyl‐d‐erythritol 4‐Phosphate Cytidylyl Transferase/2‐C‐Methyl‐d‐erythritol‐2,4‐cyclopyrophosphate Synthase (IspDF) of Helicobacter pylori

A library of over 103 thousand compounds was screened for inhibitors of the IspD domain (2‐C‐methyl‐d ‐erythritol 4‐phosphate cytidylyl transferase domain) of the bifunctional IspDF protein from Helicobacter pylori using a photometric assay. Around 300 compounds showed IC₅₀ values below 100 μm , and three compounds had IC₅₀ values below 1 μm . A few IspD inhibitors could also inhibit the IspF domain (2‐C‐Methyl‐d ‐erythritol‐2,4‐cyclopyrophosphate synthase) of the IspDF protein. The most potent IspD inhibitors were tested as growth inhibitors of H. pylori. Several compounds showed inhibition of bacterial growth with IC₅₀ in the single‐digit μm range. The most potent growth inhibitor had an IC₅₀ value of 3.4 μm . The most potent growth inhibitor without measurable effect on eukaryotic cell viability had an IC₅₀ value of 7.2 μm .     

Liquid-liquid extraction and separation studies of uranium(vi)

Summary Separation of uranium(VI) from iron(III), molybdenum(VI), vanadium (V), bismuth(III), zirconium(IV) and thorium(IV) is achieved by liquid-liquid extraction with 4-methyl-3-pentene-2-one (mesityl oxide; MeO) from sodium salicylate media (0.1M, pH 6.0). The extracted species is UO₂(HO·C₆H₄COO)₂·2MeO. A procedure for separating 50g of uranium from mg amounts of the other metals is described.

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Flüssig-flüssig-Extraktion und Trennung von Uran(VI)

Zusammenfassung Die Trennung des U(VI) von Fe(III), Mo(VI), V(V), Bi(III), Zr(IV) und Th(IV) läßt sich durch Flüssig-flüssig-Extraktion mit 4-Methyl-3-penten-2-on] (Mesityloxid, MeO) aus 0,1M Natriumsalicylat bei pH 6,0 durchführen. Die extrahierte Verbindung ist UO₂(HO·C₆H₄COO)2·2MeO. Ein Verfahren zur Abtrennung von 50g Uran von Milligrammengen der anderen Metalle wurde beschrieben.

     

Structure-guided fragment-based<Emphasis Type="Italic"> in silico</Emphasis> drug design of dengue protease inhibitors

An in silico fragment-based drug design approach was devised and applied towards the identification of small molecule inhibitors of the dengue virus (DENV) NS2B-NS3 protease. Currently, no DENV protease co-crystal structure with bound inhibitor and fully formed substrate binding site is available. Therefore a homology model of DENV NS2B-NS3 protease was generated employing a multiple template spatial restraints method and used for structure-based design. A library of molecular fragments was derived from the ZINC screening database with help of the retrosynthetic combinatorial analysis procedure (RECAP). 150,000 molecular fragments were docked to the DENV protease homology model and the docking poses were rescored using a target-specific scoring function. High scoring fragments were assembled to small molecule candidates by an implicit linking cascade. The cascade included substructure searching and structural filters focusing on interactions with the S1 and S2 pockets of the protease. The chemical space adjacent to the promising candidates was further explored by neighborhood searching. A total of 23 compounds were tested experimentally and two compounds were discovered to inhibit dengue protease (IC₅₀ = 7.7 μM and 37.9 μM, respectively) and the related West Nile virus protease (IC₅₀ = 6.3 μM and 39.0 μM, respectively). This study demonstrates the successful application of a structure-guided fragment-based in silico drug design approach for dengue protease inhibitors providing straightforward hit generation using a combination of homology modeling, fragment docking, chemical similarity and structural filters.     

Rapid discovery of inhibitors of <Emphasis Type="Italic">Toxoplasma gondii</Emphasis> using hybrid structure-based computational approach

Toxoplasma (T.) gondii, the causative agent of toxoplasmosis, is a ubiquitous opportunistic pathogen that infects individuals worldwide, and is a leading cause of severe congenital neurologic and ocular disease in humans. No vaccine to protect humans is available, and hypersensitivity and toxicity limit the use of the few available medicines. Therefore, safer and more effective medicines to treat toxoplasmosis are urgently needed. Using the Hybrid Structure Based (HSB) method, we have previously identified small molecule inhibitors of P. falciparum that seem to target a novel protein–protein interaction between the Myosin tail interacting protein and myosin light chain. This pathway has been hypothesized to be involved in invasion of host erythrocytes by the parasite and is broadly conserved among the apicomplexans. Guided by similar computational drug design approaches, we investigated this series of small molecules as potential inhibitors of T. gondii. Compound C3-21, identified as the most active inhibitor in this series, exhibited an IC₅₀ value ~500 nM against T. gondii. Among the 16 structural analogs of C3-21 tested thus far, nine additional compounds were identified with IC₅₀ values <10.0 μM. In vitro assays have revealed that C3-21 markedly limits intracellular growth of T. gondii tachyzoites, but has no effect on host cell human foreskin fibroblasts (HFF) at concentrations more than a log greater than the concentration that inhibits the parasites.