Screening of benzamidine-based thrombin inhibitors via a linear interaction energy in continuum electrostatics model

Abstract  

A series of 27 benzamidine inhibitors covering a wide range of biological activity and chemical diversity was analysed to derive a Linear Interaction Energy in Continuum Electrostatics (LIECE) model for analysing the thrombin inhibitory activity. The main interactions occurring at the thrombin binding site and the preferred binding conformations of inhibitors were explicitly biased by including into the LIECE model 10 compounds extracted from X-ray solved thrombin-inhibitor complexes available from the Protein Data Bank (PDB). Supported by a robust statistics (r ² = 0.698; q ² = 0.662), the LIECE model was successful in predicting the inhibitory activity for about 76% of compounds (r _ext² ≥ 0.600) from a larger external test set encompassing 88 known thrombin inhibitors and, more importantly, in retrieving, at high sensitivity and with better performance than docking and shape-based methods, active compounds from a thrombin combinatorial library of 10240 mimetic chemical products. The herein proposed LIECE model has the potential for successfully driving the design of novel thrombin inhibitors with benzamidine and/or benzamidine-like chemical structure.     

Bioassay-Guided Fractionation of Erythrostemon yucatanensis (Greenm.) Gagnon & GP Lewis Components with Anti-hemagglutinin Binding Activity against Influenza A/H1N1 Virus

Erythrostemon yucatanensis (Greenm.) Gagnon & GP Lewis is a legume tree native to and widely distributed in southeast Mexico, where its branches are used in traditional medicine. An in vitro evaluation of the antiviral activity of extracts and fractions from the leaves, stem bark and roots against two strains of the AH1N1 influenza virus was performed, leading to the identification of bioactive compounds in this medicinal plant. In a cytopathic effect reduction assay, the fractions from the leaves and stem bark were the active elements at the co-treatment level. These were further fractionated based on their hemagglutination inhibition activity. The analysis of spectroscopy data identified a combination of phytosterols (β-sitosterol, stigmasterol and campesterol) in the stem bark active fraction as the main anti-hemagglutinin binding components, while 5-hydroxy-2(2-hydroxy-3,4,5-trimethoxyphenyl)-7-metoxi-4H(chromen-4-ona), which was isolated from the leaf extracts, showed a weak inhibition of viral hemagglutinin. Time of addition experiments demonstrated that the mixture of sterols had a direct effect on viral particle infectivity at the co-treatment level (IC50 = 3.125 µg/mL). This effect was also observed in the virus plaque formation inhibition assay, where the mixture showed 90% inhibition in the first 20 min of co-treatment at the same concentration. Additionally, it was found using qRT-PCR that the NP copy number was reduced by 92.85% after 60 min of co-treatment. These results are the first report of components with anti-hemagglutinin binding activity in the genus Erythrostemon sp.     

5-Aza-2′-Deoxycytidine and Valproic Acid in Combination with CHIR99021 and A83-01 Induce Pluripotency Genes Expression in Human Adult Somatic Cells

A generation of induced pluripotent stem cells (iPSC) by ectopic expression of OCT4, SOX2, KLF4, and c-MYC has established promising opportunities for stem cell research, drug discovery, and disease modeling. While this forced genetic expression represents an advantage, there will always be an issue with genomic instability and transient pluripotency genes reactivation that might preclude their clinical application. During the reprogramming process, a somatic cell must undergo several epigenetic modifications to induce groups of genes capable of reactivating the endogenous pluripotency core. Here, looking to increase the reprograming efficiency in somatic cells, we evaluated the effect of epigenetic molecules 5-aza-2′-deoxycytidine (5AZ) and valproic acid (VPA) and two small molecules reported as reprogramming enhancers, CHIR99021 and A83-01, on the expression of pluripotency genes and the methylation profile of the OCT4 promoter in a human dermal fibroblasts cell strain. The addition of this cocktail to culture medium increased the expression of OCT4, SOX2, and KLF4 expression by 2.1-fold, 8.5-fold, and 2-fold, respectively, with respect to controls; concomitantly, a reduction in methylated CpG sites in OCT4 promoter region was observed. The epigenetic cocktail also induced the expression of the metastasis-associated gene S100A4. However, the epigenetic cocktail did not induce the morphological changes characteristic of the reprogramming process. In summary, 5AZ, VPA, CHIR99021, and A83-01 induced the expression of OCT4 and SOX2, two critical genes for iPSC. Future studies will allow us to precise the mechanisms by which these compounds exert their reprogramming effects.     

Simple solar cells of 3.5% efficiency with antimony sulfide‐selenide thin films

Thin films of antimony sulfide‐selenide solid solutions (Sb₂S_x Se_3–x) were prepared by chemical bath deposition and thermal evaporation to constitute solar cells of a transparent conductive oxide (FTO)/CdS/Sb₂S_x Se_3–x/C–Ag. The cell parameters vary depending on the sulfide‐selenide composition in the films. The best solar cell efficiency of 3.6% was obtained with a solid solution Sb₂S_1.5Se_1.5 prepared by thermal evaporation of the precipitate for which the open circuit voltage is 0.52 V and short circuit current density, 15.7 mA/cm²under AM 1.5G (1000 W/m²) solar radiation. For all‐chemically deposited solar cells of Sb₂S_1.1Se_1.9 absorber, these values are: 2.7%, 0.44 V, and 15.8 mA/cm², and for Sb₂S_0.8Se_2.2, they are: 2.5%, 0.38 V and 18 mA/cm². (© 2016 WILEY‐VCH Verlag GmbH &Co. KGaA, Weinheim)     

The discontinuous Galerkin method with reduced integration scheme for the boundary terms in almost incompressible linear elasticity

In this paper, the discontinuous Galerkin (dG) method is introduced and applied for a problem of nearly incompressible material behavior, where the standard finite element method, namely the conventional continuous Galerkin (cG) method faces the well-known problem of volumetric locking. The highlight of the work lies in the reduced integration scheme for the boundary terms of the dG method. Two different reduced and mixed integration schemes are presented and applied to reduce the calculation time. The dG method converges much faster than standard cG method with respect to the number of the elements, provided that the penalty value is sufficiently large. (© 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim)     

Identification of structural alerts for liver and kidney toxicity using repeated dose toxicity data

Background

The potential for a compound to cause hepatotoxicity and nephrotoxicity is a matter of extreme interest for human health risk assessment. To assess liver and kidney toxicity, repeated-dose toxicity (RDT) studies are conducted mainly on rodents. However, these tests are expensive, time-consuming and require large numbers of animals. For early toxicity screening, in silico models can be applied, reducing the costs, time and animals used. Among in silico approaches, structure–activity relationship (SAR) methods, based on the identification of chemical substructures (structural alerts, SAs) related to a particular activity (toxicity), are widely employed.

Results

We identified and evaluated some SAs related to liver and kidney toxicity, using RDT data on rats taken from the hazard evaluation support system (HESS) database. We considered only SAs that gave the best percentages of true positives (TP).

Conclusions

It was not possible to assign an unambiguous mode of action for all the SAs, but a mechanistic explanation is provided for some of them. Such achievements may help in the early identification of liver and renal toxicity of substances.

     

UV-photocrosslinking of inulin derivatives to produce hydrogels for drug delivery application

In this work, INU, a natural polysaccharide, has been chemically modified in order to obtain new photocrosslinkable derivatives. To reach this goal, INU has been derivatized with MA thus obtaining four samples (INU-MA derivatives) as a function of the temperature and time of reaction. An aqueous solution of the derivative INU-MA1 was irradiated by using a UV lamp with an emission range from 250 to 364 nm and without using photoinitiators. The obtained hydrogel showed a remarkable water affinity but it underwent a partial degradation in simulated gastric fluid. To overcome this drawback, INU-MA1 was derivatized with SA thus obtaining the INU-MA1-SA derivative designed to produce a hydrogel showing a low swelling and an increased chemical stability in acidic medium. Ibuprofen, as a model drug, was loaded by soaking into INU-MA1 and INU-MA1-SA hydrogels and its release from these matrices was evaluated in simulated gastrointestinal fluids. INU-MA1 hydrogel showed the ability to quickly release the entrapped drug thus indicating its potential as a matrix for an oral formulation. INU-MA1-SA hydrogel showed a pH-responsive drug delivery. Therefore it is a promising candidate for controlled drug release in the intestinal tract.     

Dual Role of the 1,2,3‐Triazolium Ring as a Hydrogen‐Bond Donor and Anion–π Receptor in Anion‐Recognition Processes

Several bis(triazolium)‐based receptors have been synthesized as chemosensors for anion recognition. The central naphthalene core features two aryltriazolium side‐arms. NMR experiments revealed differences between the binding modes of the two triazolium rings: one triazolium ring acts as a hydrogen‐bond donor, the other as an anion–π receptor. Receptors 9²⁺?2BF₄ ^? (C₆H₅), 11²⁺?2BF₄ ^? (4‐NO₂?C₆H₄), and 13²⁺?2BF^4? (ferrocenyl) bind HP₂O₇^3? anions in a mixed‐binding mode that features a combination of hydrogen‐bonding and anion–π interactions and results in strong binding. On the other hand, receptor 10²⁺?2 BF₄ ^? (4‐CH₃O?C₆H₄) only displays combined Csp₂?H/anion–π interactions between the two arms of the receptors and the bound anion rather than triazolium (CH)⁺???anion hydrogen bonding. All receptors undergo a downfield shift of the triazolium protons, as well as the inner naphthalene protons, in the presence of H₂PO₄^? anions. That suggests that only hydrogen‐bonding interactions exist between the binding site and the bound anion, and involve a combination of cationic (triazolium) and neutral (naphthalene) C?H donor interactions. Theoretical calculations relate the electronic structure of the substituent on the aromatic group with the interaction energies and provide a minimum‐energy conformation for all the complexes that explains their measured properties.     

Secondary interactions in n‐(chloromethyl)pyridinium chlorides (n = 2, 3, 4)

In the isomeric title compounds, viz. 2‐, 3‐ and 4‐(chloro­methyl)pyridinium chloride, C₆H₇ClN⁺·Cl^?, the secondary interactions have been established as follows. Classical N—H?Cl^? hydrogen bonds are observed in the 2‐ and 3‐isomers, whereas the 4‐isomer forms inversion‐symmetric N—H(?Cl^??)₂H—N dimers involving three‐centre hydrogen bonds. Short Cl?Cl contacts are formed in both the 2‐isomer (C—Cl?Cl^?, approximately linear at the central Cl) and the 4‐isomer (C—Cl?Cl—C, angles at Cl of ca 75°). Additionally, each compound displays contacts of the form C—H?Cl, mainly to the Cl^? anion. The net effect is to create either a layer structure (3‐isomer) or a three‐dimensional packing with easily identifiable layer substructures (2‐ and 4‐isomers).