Discovery of an Acyclic Nucleoside Phosphonate that Inhibits Mycobacterium tuberculosis ThyX Based on the Binding Mode of a 5‐Alkynyl Substrate Analogue

The urgent need for new antibiotics poses a challenge to target un(der)exploited vital cellular processes. Thymidylate biosynthesis is one such process due to its crucial role in DNA replication and repair. Thymidylate synthases (TS) catalyze a crucial step in the biosynthesis of thymidine 5‐triphosphate (TTP), an elementary building block required for DNA synthesis and repair. To date, TS inhibitors have only been successfully applied in anticancer therapy due to their lack of specificity for antimicrobial versus human enzymes. However, the discovery of a new family of TS enzymes (ThyX) in a range of pathogenic bacteria that is structurally and biochemically different from the “classic” TS (ThyA) has opened the possibility to develop selective ThyX inhibitors as potent antimicrobial drugs. Here, the interaction of the known inhibitor 5‐(3‐octanamidoprop‐1yn‐1yl)‐2′‐deoxyuridine‐5′‐monophosphate ( 1 ) with Mycobacterium tuberculosis ThyX enzyme is explored using molecular modeling starting from published crystal structures, with further confirmation through NMR experiments. While the deoxyuridylate (dUMP) moiety of compound 1 occupies the cavity of the natural substrate in ThyX, the rest of the ligand (the “5‐alkynyl tail”) extends to the outside of the enzyme between two of its four subunits. The hydrophobic pocket that accommodates the alkyl part of the tail is formed by displacement of Tyr 44.C, Tyr 108.A and Lys 165.A. Changes to the resonance of the Lys 165 NH₃ group upon ligand binding were monitored in a titration experiment by 2D HISQC NMR. Guided by the results of the modeling and NMR studies, and inspired by the success of acyclic antiviral nucleosides, compounds where a 5‐alkynyl uracyl moiety is coupled to an acyclic nucleoside phosphonate (ANP) were synthesized and evaluated. Of the compounds evaluated, sodium (6‐(5‐(3‐octanamidoprop‐1‐yn‐1‐yl)‐2,4‐dioxo‐3,4‐dihydropyrimidin‐1(2H)‐yl)hexyl)phosphonate ( 3 e ) exhibited 43 % of inhibitory effect on ThyX at 50 μM . While only modest activity was achieved, this is the first example of an ANP inhibiting ThyX, and these results can be used to further guide structural modifications to this class to develop more potent compounds with potential application as antibacterial agents acting through a novel mechanism of action.     

On the simultaneous description of h‐bonding and dipolar interactions with point charges in force field models

H‐bonding and polar interactions occur together in real fluids, but are of different nature and have different effects on macroscopic properties. Nevertheless, both are usually described by point charges in force field models. Despite this, the two effects can be separated. A simple model fluid is studied: a single Lennard‐Jones (LJ) site with two opposing point charges q placed in the center of the LJ site and at a distance d. By suitably varying both d and q, the dipole moment μ is kept constant. Both μ and d are systematically varied to study the properties of the resulting models, including H‐bonding, which is determined using a geometric criterion from literature. d can be used for tuning the H‐bonding strength and, thus, polarity and H‐bonding can be adjusted individually. The study of a second related model with symmetrically positioned point charges does not reveal this separation. © 2015 American Institute of Chemical Engineers AIChE J, 61: 2926–2932, 2015     

High‐Fidelity Recognition of RNA: Solution Structure of a DNA:RNA Hybrid Duplex with a Molecular Cap

Binding RNA targets, such as microRNAs, with high fidelity is challenging, particularly when the nucleobases to be bound are located at the terminus of the duplex between probe and target. Recently, a peptidyl chain terminating in a quinolone, called ogOA, was shown to act as a cap that enhances affinity and fidelity for RNAs, stabilizing duplexes with Watson–Crick pairing at their termini. Here we report the three‐dimensional structure of an intramolecular complex between a DNA strand featuring the ogOA cap and an RNA segment, solved by NMR and restrained torsion angle molecular dynamics. The quinolone stacks on the terminal base pair of the hybrid duplex, positioned by the peptidyl chain, whose prolinol residue induces a sharp bend between the 5′ terminus of the DNA chain and the glycine linked to the oxolinic acid residue. The structure explains why canonical base pairing is favored over hard‐to‐suppress mismatched base combinations, such as T:G and A:A, and helps to design improved high‐fidelity probes for RNA.     

Modulation of CD14 and TLR4⋅MD‐2 Activities by a Synthetic Lipid A Mimetic

Monosaccharide lipid A mimetics based on a glucosamine core linked to two fatty acid chains and bearing one or two phosphate groups have been synthesized. Compounds 1 and 2 , each with one phosphate group, were practically inactive in inhibiting LPS‐induced TLR4 signaling and cytokine production in HEK‐blue cells and murine macrophages, but compound 3 , with two phosphate groups, was found to be active in efficiently inhibiting TLR4 signal in both cell types. The direct interaction between compound 3 and the MD‐2 coreceptor was investigated by NMR spectroscopy and molecular modeling/docking analysis. This compound also interacts directly with the CD14 receptor, stimulating its internalization by endocytosis. Experiments on macrophages show that the effect on CD14 reinforces the activity on MD‐2 ? TLR4 because compound 3 's activity is higher when CD14 is important for TLR4 signaling (i.e., at low LPS concentration). The dual targeting of MD‐2 and CD14, accompanied by good solubility in water and lack of toxicity, suggests the use of monosaccharide 3 as a lead compound for the development of drugs directed against TLR4related syndromes.     

Determination of Ni and Zn in an Oil Matrix using Schiff Base‐Assisted Extraction Followed by a Flame Atomic Absorption Spectrometer: A Simple Strategy to Determine Ni and Zn

In the present work, a new and simple Schiff base‐assisted extraction strategy for Ni and Zn from an edible oil matrix with subsequent determination using a flame atomic absorption spectrometer was suggested. According to the green approach, laborious sample‐pretreatment procedures were eliminated via complexation of the analytes with N,N′‐bis(4‐methoxysalycylidene)‐2‐hydroxy‐1,3‐propanediamine (4MSHP) and transferred from the oil phase to the aqueous phase. The complexation properties of 4MSHP, Ni, and Zn were investigated using UV–vis spectrophotometry. The experimental conditions that affect the extraction efficiency were optimized using central composite design. The optimum conditions for the extraction of Ni and Zn were as follows: a volume to oil mass ratio of 0.83 to 1.31 mL g^?1 of 4MSHP solution; 62.3‐ and 50.6‐min, stirring time; 27.3 and 31.1 °C, temperature, respectively. The detection limits (3s_bm^?1) were 0.41 μg g^?1 for Ni and 0.16 μg g^?1 for Zn. Validation of the suggested work was performed by the analysis of organometallic standard‐doped n‐hexane solutions as certified reference materials under the optimum experimental conditions. The recovery percentages were warranted the accuracy and found as 98.2 ± 1.8% for Ni and 99.8 ± 1.2% for Zn. In addition, relative SD values were below 5% for both the analytes. The Student's t‐test showed that there was no significant difference between the found and doped amount of analytes at 95% confidence level. The features such as the detection technique, cheapness, eco‐friendly solvent usage, and practicality were better compared to the literature.