Natural product-inspired cascade synthesis yields modulators of centrosome integrity

In biology-oriented synthesis, the scaffolds of biologically relevant compound classes inspire the synthesis of focused compound collections enriched in bioactivity. This criterion is, in particular, met by the scaffolds of natural products selected in evolution. The synthesis of natural product-inspired compound collections calls for efficient reaction sequences that preferably combine multiple individual transformations in one operation. Here we report the development of a one-pot, twelve-step cascade reaction sequence that includes nine different reactions and two opposing kinds of organocatalysis. The cascade sequence proceeds within 10-30 min and transforms readily available substrates into complex indoloquinolizines that resemble the core tetracyclic scaffold of numerous polycyclic indole alkaloids. Biological investigation of a corresponding focused compound collection revealed modulators of centrosome integrity, termed centrocountins, which caused fragmented and supernumerary centrosomes, chromosome congression defects, multipolar mitotic spindles, acentrosomal spindle poles and multipolar cell division by targeting the centrosome-associated proteins nucleophosmin and Crm1.     

Binding of Lipoic Acid Induces Conformational Change and Appearance of a New Binding Site in Methylglyoxal Modified Serum Albumin

The binding of lipoic acid (LA), to methylglyoxal (MG) modified BSA was studied using isothermal titration calorimetry in combination with enzyme kinetics and molecular modelling. The binding of LA to BSA was sequential with two sites, one with higher binding constant and another comparatively lower. In contrast the modified protein showed three sequential binding sites with a reduction in affinity at the high affinity binding site by a factor of 10. CD results show appreciable changes in conformation of the modified protein as a result of binding to LA. The inhibition of esterase like activity of BSA by LA revealed that it binds to site II in domain III of BSA. The pH dependence of esterase activity of native BSA indicated a catalytic group with a pK(a) = 7.9 +/- 0.1, assigned to Tyr411 with the conjugate base stabilised by interaction with Arg410. Upon modification by MG, this pK(a) increased to 8.13. A complex obtained by docking of LA to BSA and BSA in which Arg410 is modified to hydroimidazolone showed that the long hydrocarbon chain of lipoic acid sits in a cavity different from the one observed for unmodified BSA. The molecular electrostatic potential showed that the modification of Arg410 reduced the positive electrostatic potential around the protein-binding site. Thus it can be concluded that the modification of BSA by MG resulted in altered ligand binding characteristics due to changes in the internal geometry and electrostatic potential at the binding site.     

Detailed protein sequence alignment based on Spectral Similarity Score (SSS)

Background  

The chemical property and biological function of a protein is a direct consequence of its primary structure. Several algorithms have been developed which determine alignment and similarity of primary protein sequences. However, character based similarity cannot provide insight into the structural aspects of a protein. We present a method based on spectral similarity to compare subsequences of amino acids that behave similarly but are not aligned well by considering amino acids as mere characters. This approach finds a similarity score between sequences based on any given attribute, like hydrophobicity of amino acids, on the basis of spectral information after partial conversion to the frequency domain.     

All-atom molecular dynamics simulations of an artificial sodium channel in a lipid bilayer: the effect of water solvation/desolvation of the sodium ion

All-atom molecular dynamics is used to investigate the transport of Na⁺ across a 1,2-dioleoyl-sn-glycero-3-phosphocholine lipid bilayer facilitated by a diazacrown hydraphile. Specifically, the free energy of Na⁺ passing through the bilayer is calculated using the adaptive biasing force method to study the free energy associated with the increase in Na⁺ transport in the presence of the hydraphile molecule. The results show that water interaction greatly influences Na⁺ transport through the lipid bilayer as water is pulled through the bilayer with Na⁺ forming a water channel. The hydraphile causes a reduction in the free energy barrier for the transport of Na⁺ through the head group part of the lipid bilayer since it complexes the Na⁺ reducing the necessity for water to be complexed and, therefore, dragged through with Na⁺, an energetically unfavorable process. The free energy associated with Na⁺ being desolvated within the bilayer is significantly decreased in the presence of the hydraphile molecule; the hydraphile increases the number of solvation states of Na⁺ that can be adopted, and this increase in the number of available configurations provides an entropic explanation for the success of the hydraphile.     

Turning off NADPH oxidase-2 by impeding p67phox activation in infected mouse macrophages reduced viral entry and inflammation

Background

Targeting cells of the host immune system is a promising approach to fight against Influenza A virus (IAV) infection. Macrophage cells use the NADPH oxidase-2 (NOX2) enzymatic complex as a first line of defense against pathogens by generating superoxide ions O₂^– and releasing H₂O₂. Herein, we investigated whether targeting membrane -embedded NOX2 decreased IAV entry via raft domains and reduced inflammation in infected macrophages.

Estimating synonymous and nonsynonymous substitution rates

Partitioning the total substitution rate into synnonymous and nonsynonymous components is a key aspect of many analyses in molecular evolution. Numerous methods exist for estimating these rates. However, until recently none of the estimation procedures were based on a sound statistical footing. In this paper, the evolutionary model of Muse and Gaut (1994) is used as the basis for two sets of parameters quantifying silent and replacement substitution rates. The parameters are shown to be equal when the four nucleotides are equally frequent and unequal otherwise. Maximum-likelihood estimation of these parameters is described, and the performance of these estimates is compared to that of existing estimation procedures. It is shown that the estimates of Nei and Gojobori (1986) are not unbiased for either set of parameters, although they provide very good estimates for one set as long as sequence divergence is not too high. However, some disturbing properties are found for the Nei and Gojobori estimates. In particular, it is shown that the expected value of the Nei and Gojobori estimate of silent substitution rate is a function of both the silent and replacement substitution rates. The maximum-likelihood estimates have no such problems.      

miR-184 Regulates Pancreatic β-Cell Function According to Glucose Metabolism

In response to fasting or hyperglycemia, the pancreatic β-cell alters its output of secreted insulin; however, the pathways governing this adaptive response are not entirely established. Although the precise role of microRNAs (miRNAs) is also unclear, a recurring theme emphasizes their function in cellular stress responses. We recently showed that miR-184, an abundant miRNA in the β-cell, regulates compensatory proliferation and secretion during insulin resistance. Consistent with previous studies showing miR-184 suppresses insulin release, expression of this miRNA was increased in islets after fasting, demonstrating an active role in the β-cell as glucose levels lower and the insulin demand ceases. Additionally, miR-184 was negatively regulated upon the administration of a sucrose-rich diet in Drosophila, demonstrating strong conservation of this pathway through evolution. Furthermore, miR-184 and its target Argonaute2 remained inversely correlated as concentrations of extracellular glucose increased, underlining a functional relationship between this miRNA and its targets. Lastly, restoration of Argonaute2 in the presence of miR-184 rescued suppression of miR-375-targeted genes, suggesting these genes act in a coordinated manner during changes in the metabolic context. Together, these results highlight the adaptive role of miR-184 according to glucose metabolism and suggest the regulatory role of this miRNA in energy homeostasis is highly conserved.     

Quinolidene based monocarbonyl curcumin analogues as promising antimycobacterial agents: Synthesis and molecular docking study

A series of quinoline incorporated monocarbonyl curcumin analogues was efficiently synthesized using [HDBU][HSO₄] as catalyst via Knoevenagel type condensation and evaluated for their in vitro antitubercular activity against Mycobacterium tuberculosis H37Ra (MTB) and Mycobacterium bovis BCG in dormant state. The analogues 3e, 3h, 4a and 4e exhibited very good antitubercular activity. The antiproliferative activity of the analogues against MCF-7, A549 and HCT-116 cell lines was evaluated using modified MTT assay and these compounds were found to be non-cytotoxic. Molecular docking study has been carried out against M. tuberculosis pantothenate synthetase (MTB PS) enzyme in an effort to enhance the understanding of their action as antitubercular agents. The potency, low cytotoxicity and selectivity of these analogues support them as valid leads for further optimization.     

Degradation of dibenzothiophene and its metabolite 3-hydroxy-2-formylbenzothiophene by an environmental isolate

Microbial degradation of dibenzothiophene (DBT) beyond 3-hydroxy-2-formylbenzothiophene (HFBT), a commonly detected metabolite of the Kodama pathway for DBT metabolism, and the catabolic intermediates leading to its mineralization are not fully understood. The enrichment cultures cultivated from crude oil contaminated soil led to isolation of ERI-11; a natural mixed culture, selected for its ability to deplete DBT in basal salt medium (BSM). A bacterial strain isolated from ERI-11, and tentatively named A₁₁, degraded more than 90 % of the initial DBT (270 µM), present as the sole carbon and sulfur source, in 72 h. Gas chromatography–mass spectrophotometry (GC–MS) analyses of the DBT degrading A₁₁ culture medium extracts led to detection of HFBT. The metabolite HFBT, produced using A₁₁, was used in degradation assays to evaluate its metabolism by the bacteria isolated in this study. Ultra violet–visible spectrophotometry and high-performance liquid chromatography analyses established the ability of the strain A₁₁ to deplete HFBT, present as the sole sulfur and carbon source in BSM. GC–MS analyses showed the presence of 2-mercaptobenzoic acid in the HFBT degrading A₁₁ culture extracts. The findings in this study establish that the environmental isolate A₁₁ possesses the metabolic capacity to degrade DBT beyond the metabolite HFBT. The compound 2-mercaptobenzoic acid is an intermediate formed on HFBT degradation by A₁₁.     

Quinoline Based Monocarbonyl Curcumin Analogs as Potential Antifungal and Antioxidant Agents: Synthesis,Bioevaluation and Molecular Docking Study

In search for new fungicidal and free radical scavenging agents, we synthesized a focused library of 2‐chloroquinoline based monocarbonyl analogs of curcumin (MACs). The synthesized MACs were evaluated for in vitro antifungal and antioxidant activity. The antifungal activity was evaluated against five different fungal strains such as Candida albicans, Fusarium oxysporum, Aspergillus flavus, Aspergillus niger, and Cryptococcus neoformans, respectively. Most of the synthesized MACs displayed promising antifungal activity compared to the standard drug Miconazole. Furthermore, molecular docking study on a crucial fungal enzyme sterol 14α‐demethylase (CYP51) could provide insight into the plausible mechanism of antifungal activity. MACs were also screened for in vitro radical scavenging activity using butylated hydroxytoluene (BHT) as a standard. Almost all MACs exhibited better antioxidant activity compared to BHT.