Interplay between R513 methylation and S516 phosphorylation of the cardiac voltage-gated sodium channel

Arginine methylation is a novel post-translational modification within the voltage-gated ion channel superfamily, including the cardiac sodium channel, Naᵥ1.5. We show that Naᵥ1.5 R513 methylation decreases S516 phosphorylation rate by 4 orders of magnitude, the first evidence of protein kinase A inhibition by arginine methylation. Reciprocally, S516 phosphorylation blocks R513 methylation. Naᵥ1.5 p.G514C, associated to cardiac conduction disease, abrogates R513 methylation, while leaving S516 phosphorylation rate unchanged. This is the first report of methylation–phosphorylation cross-talk of a cardiac ion channel

La importància de les eines computacionals en el disseny d'enzims d'interès industrial

El camp del disseny d'enzims té com a principal objectiu el desenvolupament d'enzims modificats per tal d'accelerar noves reaccions o d'acceptar substrats no naturals. Tot i els avenços en el camp, encara no s'ha assolit el disseny rutinari d'enzims. L'evolució dirigida (DE) és una de les estratègies més poderoses que existeixen, però el seu alt cost i el fet de ser una estratègia no racional en limita l'aplicació. La comprensió de com l'evolució dirigida és capaç d'obtenir variants altament actives és crucial per al futur desenvolupament de protocols computacionals robusts capaços de predir amb precisió quins canvis d'aminoàcids són necessaris per a tenir alta activitat enzimàtica. En aquest treball, es demostra la importància dels mètodes computacionals, en particular, els basats en simulacions de dinàmica molecular, per a elucidar l'efecte de mutacions al centre actiu i a posicions llunyanes en l'activitat i selectivitat enzimàtica.The enzyme design field pursues the development of new modified enzyme variants to target new synthetically useful reactions and/or substrates. Although many advances have been made, the routine design of enzymes has not yet been achieved. Directed evolution (DE) is one of the most powerful strategies that exist to that end but its high cost and the fact that it is not rational limit its application. The understanding of how DE is able to provide highly active variants is crucial to the future development of robust computational protocols capable of accurately predicting which amino acid changes are required for high enzymatic activity. In this paper, we show the important role of computational methods, in particular molecular dynamics (MD) simulations, for elucidating the effect of distal and active site mutations that lead to enhanced enzymatic activity and selectivity

Sponge-like molecular cage for purification of fullerenes

Since fullerenes are available in macroscopic quantities from fullerene soot, large efforts have been geared toward designing efficient strategies to obtain highly pure fullerenes, which can be subsequently applied in multiple research fields. Here we present a supramolecular nanocage synthesized by metal-directed self-assembly, which encapsulates fullerenes of different sizes. Direct experimental evidence is provided for the 1:1 encapsulation of C 60, C 70, C 76, C 78 and C 84, and solid state structures for the host-guest adducts with C 60 and C 70 have been obtained using X-ray synchrotron radiation. Furthermore, we design a washing-based strategy to exclusively extract pure C 60 from a solid sample of cage charged with a mixture of fullerenes. These results showcase an attractive methodology to selectively extract C 60 from fullerene mixtures, providing a platform to design tuned cages for selective extraction of higher fullerenes. The solid-phase fullerene encapsulation and liberation represent a twist in host-guest chemistry for molecular nanocage structures

Insights into the molecular determinants of thermal stability in halohydrin dehalogenase HheD2

Halohydrin dehalogenases (HHDHs) are promising enzymes for application in biocatalysis due to their promiscuous epoxide ring-opening activity with various anionic nucleophiles. So far, seven different HHDH subtypes A to G have been reported with subtype D containing the by far largest number of enzymes. Moreover, several characterized members of subtype D have been reported to display outstanding characteristics such as high catalytic activity, broad substrate spectra or remarkable thermal stability. Yet, no structure of a D-type HHDH has been reported to date that could be used to investigate and understand those features on a molecular level. We therefore solved the crystal structure of HheD2 from gamma proteobacterium HTCC2207 at 1.6 Å resolution and used it as a starting point for targeted mutagenesis in combination with molecular dynamics (MD) simulation, in order to study the low thermal stability of HheD2 in comparison with other members of subtype D. This revealed a hydrogen bond between conserved residues Q160 and D198 to be connected with a high catalytic activity of this enzyme. Moreover, a flexible surface region containing two α-helices was identified to impact thermal stability of HheD2. Exchange of this surface region by residues of HheD3 yielded a variant with 10 °C higher melting temperature and reaction temperature optimum. Overall, our results provide important insights into the structure-function relationship of HheD2 and presumably for other D-type HHDHs. DATABASES: Structural data are available in PDB database under the accession number 7B73

Protein-directed crystalline 2D fullerene assemblies

Water soluble 2D crystalline monolayers of fullerenes grow on planar assemblies of engineered consensus tetratricopeptide repeat proteins. Designed fullerene-coordinating tyrosine clamps on the protein introduce specific fullerene binding sites, which facilitate fullerene nucleation. Through reciprocal interactions between the components, the hybrid material assembles into two-dimensional 2 nm thick structures with crystalline order, that conduct photo-generated charges. Thus, the protein-fullerene hybrid material is a demonstration of the developments toward functional materials with protein-based precision control of functional elements

Mutational Landscape and tumor burden assessed by cell-free DNA in Diffuse Large B-Cell Lymphoma in a population-based study

Purpose: We analyzed the utility of cell-free DNA (cfDNA) in a prospective population-based cohort to determine the mutational profile, assess tumor burden, and estimate its impact in response rate and outcome in patients with diffuse large B-cell lymphoma (DLBCL). Experimental design: A total of 100 patients were diagnosed with DLBCL during the study period. Mutational status of 112 genes was studied in cfDNA by targeted next-generation sequencing. Paired formalin-fixed, paraffin-embedded samples and volumetric PET/CT were assessed when available. Results: Appropriate cfDNA to perform the analyses was obtained in 79 of 100 cases. At least one mutation could be detected in 69 of 79 cases (87%). The sensitivity of cfDNA to detect the mutations was 68% (95% confidence interval, 56.2-78.7). The mutational landscape found in cfDNA samples was highly consistent with that shown in the tissue and allowed genetic classification in 43% of the cases. A higher amount of circulating tumor DNA (ctDNA) significantly correlated with clinical parameters related to tumor burden (elevated lactate dehydrogenase and β2-microglobulin serum levels, advanced stage, and high-risk International Prognostic Index) and total metabolic tumor volume assessed by PET/CT. In patients treated with curative intent, high ctDNA levels (>2.5 log hGE/mL) were associated with lower complete response (65% vs. 96%; P < 0.004), shorter progression-free survival (65% vs. 85%; P = 0.038), and overall survival (73% vs. 100%; P = 0.007) at 2 years, although it did not maintain prognostic value in multivariate analyses. Conclusions: In a population-based prospective DLBCL series, cfDNA resulted as an alternative source to estimate tumor burden and to determine the tumor mutational profile and genetic classification, which have prognostic implications and may contribute to a future tailored treatment

Synthesis, in Vitro Profiling, and in Vivo Evaluation of Benzohomoadamantane-Based Ureas for Visceral Pain: A New Indication for Soluble Epoxide Hydrolase Inhibitors

The soluble epoxide hydrolase (sEH) has been suggested as a pharmacological target for the treatment of several diseases, including pain-related disorders. Herein, we report further medicinal chemistry around new benzohomoadamantane-based sEH inhibitors (sEHI) in order to improve the drug metabolism and pharmacokinetics properties of a previous hit. After an extensive in vitro screening cascade, molecular modeling, and in vivo pharmacokinetics studies, two candidates were evaluated in vivo in a murine model of capsaicin-induced allodynia. The two compounds showed an anti-allodynic effect in a dose-dependent manner. Moreover, the most potent compound presented robust analgesic efficacy in the cyclophosphamide-induced murine model of cystitis, a well-established model of visceral pain. Overall, these results suggest painful bladder syndrome as a new possible indication for sEHI, opening a new range of applications for them in the visceral pain field

Discovery and In Vivo Proof of Concept of a Highly Potent Dual Inhibitor of Soluble Epoxide Hydrolase and Acetylcholinesterase for the Treatment of Alzheimer's Disease

With innumerable clinical failures of target-specific drug candidates for multifactorial diseases, such as Alzheimer's disease (AD), which remains inefficiently treated, the advent of multitarget drug discovery has brought a new breath of hope. Here, we disclose a class of 6-chlorotacrine (huprine)‒TPPU hybrids as dual inhibitors of the enzymes soluble epoxide hydrolase (sEH) and acetylcholinesterase (AChE), a multitarget profile to provide cumulative effects against neuroinflammation and memory impairment. Computational studies confirmed the gorge-wide occupancy of both enzymes, from the main site to a secondary site, including a so far non-described AChE cryptic pocket. The lead compound displayed in vitro dual nanomolar potencies, adequate brain permeability, aqueous solubility, and human microsomal stability and lack of neurotoxicity, and rescued memory, synaptic plasticity and neuroinflammation in an AD mouse model, after low dose chronic oral administration

Confined organization of fullerene units along high polymer chains

Conductive fullerene (C_60) units were designed to be arranged in one dimensional close contact by locally organizing them with covalent bonds in a spatially constrained manner. Combined molecular dynamics and quantum chemical calculations predicted that the intramolecular electronic interactions (i.e. charge transport) between the pendant C_60 units could be controlled by the length of the spacers linking the C_60 units and the polymer main chain. In this context, C_60 side-chain polymers with high relative degrees of polymerization up to 1220 and fullerene compositions up to 53% were synthesized by ruthenium catalyzed ring-opening metathesis polymerization of the corresponding norbornene-functionalized monomers. UV/vis absorption and photothermal deflection spectra corroborated the enhanced inter-fullerene interactions along the polymer chains. The electron mobility measured for the thin film field-effect transistor devices from the polymers was more than an order of magnitude higher than that from the monomers, as a result of the stronger electronic coupling between the adjacent fullerene units within the long polymer chains. This molecular design strategy represents a general approach to the enhancement of charge transport properties of organic materials via covalent bond-based organization