Target-Directed Azide-Alkyne Cycloaddition for Assembling HIV-1 TAR RNA Binding Ligands

The highly conserved HIV-1 transactivation response element (TAR) binds to the trans-activator protein Tat and facilitates viral replication in its latent state. The inhibition of Tat–TAR interactions by selectively targeting TAR RNA has been used as a strategy to develop potent antiviral agents. Therefore, HIV-1 TAR RNA represents a paradigmatic system for therapeutic intervention. Herein, we have employed biotin-tagged TAR RNA to assemble its own ligands from a pool of reactive azide and alkyne building blocks. To identify the binding sites and selectivity of the ligands, the in situ cycloaddition has been further performed using control nucleotide (TAR DNA and TAR RNA without bulge) templates. The hit triazole-linked thiazole peptidomimetic products have been isolated from the biotin-tagged target templates using streptavidin beads. The major triazole lead generated by the TAR RNA presumably binds in the bulge region, shows specificity for TAR RNA over TAR DNA, and inhibits Tat–TAR interactions.     

G-Protein-Coupled Receptor–Membrane Interactions Depend on the Receptor Activation State

G-protein-coupled receptors (GPCRs) are the largest family of human membrane proteins and serve as primary targets of approximately one-third of currently marketed drugs. In particular, adenosine A₁ receptor (A₁AR) is an important therapeutic target for treating cardiac ischemia–reperfusion injuries, neuropathic pain, and renal diseases. As a prototypical GPCR, the A₁AR is located within a phospholipid membrane bilayer and transmits cellular signals by changing between different conformational states. It is important to elucidate the lipid–protein interactions in order to understand the functional mechanism of GPCRs. Here, all-atom simulations using a robust Gaussian accelerated molecular dynamics (GaMD) method were performed on both the inactive (antagonist bound) and active (agonist and G-protein bound) A₁AR, which was embedded in a 1-palmitoyl-2-oleoyl-glycero-3-phosphocholine (POPC) lipid bilayer. In the GaMD simulations, the membrane lipids played a key role in stabilizing different conformational states of the A₁AR. Our simulations further identified important regions of the receptor that interacted distinctly with the lipids in highly correlated manner. Activation of the A₁AR led to differential dynamics in the upper and lower leaflets of the lipid bilayer. In summary, GaMD enhanced simulations have revealed strongly coupled dynamics of the GPCR and lipids that depend on the receptor activation state. © 2019 Wiley Periodicals, Inc.     

A concise synthesis of 2-benzoyl-1-indanones and 1-indanones from 2-aryl-1-tetralones

Abstract

Methyl-2-(3-oxo-3-aryl) benzoates derived from acid catalyzed air oxidative fragmentation of 2-aryl-1-tetralones were efficiently undergone intramolecular-Claisen condensation in the presence of potassium tertiary butoxide. The resulting 2-benzoyl-1-indanones formed in two-step ring contractions were further subjected to indium triflate mediated retro-Claisen condensation to get 1-indanones.     

An Easy Access to Oxime Ethers by Pd‐Catalyzed C—O Cross‐Coupling of Activated Aryl Bromides with Ketoximes and Chalcone Oximes

An efficient Pd‐catalyzed method for C—O cross‐coupling of ketoximes and chalcone oximes with activated aryl bromides and bromo‐chalcones has been developed. All oxime ethers were obtained in good to excellent yields by [(π‐allyl)PdCl]₂/tBuXPhos ( L7 ) catalyst system. TrixiePhos ( L11 ) was also found to be effective for the oxime coupling. This method offers an easy and smooth coupling of chalcone oximes with activated aryl bromides and bromo‐chalcones, which has not been previously explored.     

Generation and trapping of non-aromatic cycloimines via diazotization/dediazotization of N-amino cyclic amines: theoretical and experimental results

Structural Chemistry - A theoretical investigation of the model diazotization/dediazotization of N-aminopiperidine and N-aminomorpholine at the DFT (B3LYP/6-31+G(d)) level indicated that the...     

Anti-Obesity Potential of Ponciri Fructus: Effects of Extracts,Fractions and Compounds on Adipogenesis in 3T3-L1 Preadipocytes

Background: Ponciri Fructus, a crude drug consisting of the dried immature fruits of Poncirus trifoliata (L.) Raf., is a popular folk medicine used for the treatment of allergy and gastrointestinal disorders in Korea and China. In this study, the anti-adipogenic activity of extracts and isolated compounds were evaluated using 3T3-L1 preadipocytes. Methods: Dried immature fruits were extracted and fractionated into n-hexane, ethyl acetate (EtOAc), n-butanol and water-soluble fractions. The ethanol extract and fractions were tested for anti-adipogenic activity in the 3T3-L1 cell line. The active fractions (n-hexane and EtOAc fractions) were further subjected to chromatographic techniques to isolate and identify active compounds. Furthermore, the isolated compounds were evaluated for their anti-adipogenic activity. Results: Altogether, seven compounds, including two flavonoids, one phytosteroid and four coumarin derivatives, were isolated. Ethanol extract, n-hexane fraction, EtOAc fraction and three isolated compounds (phellopterin, oxypeucedanin and poncirin) showed significant anti-adipogenic activity as observed by reduced lipid deposition in differentiated 3T3-L1 cells. Further, oxypeucedanin downregulated the key adipogenic markers, such as peroxisome proliferator-activated receptors proteins γ (PPAR-γ), sterol response element binding proteins-1 (SREBP-1), CCAAT/enhancer binding proteins-α (C/EBP-α), adipocyte-specific lipid binding proteins (FABP-4), adipocyte fatty acid binding proteins (aP2), lipoprotein lipase (LPL) and leptin. Conclusion: This study indicated that the ethanol extract, hexane fraction and ethyl acetate fraction of P. trifoliata fruits possess strong anti-adipogenic activity, containing the active compounds such as phellopterin, oxypeucedanin and poncirin. Further research is recommended to explore their efficacy and safety in animal and clinical models.     

1, 3-azaphospholo[5, 1-b]thiazolines and benzothiazoles

The title compounds 3 and 7 are novel heterocyclic systems incorporating two-coordinate phosphorus. They are obtained in reasonable to good yields from the condensation of suitable 2-ethyl-3-alkylthiazolinium and -benzothiazolium bromides 2 and 6 with phosphorus trichloride in the presence of triethylamine in an aprotic solvent. Intermediate dichlorophosphino-substituted N-ylides can be observed or isolated in some cases. From a 2-methyl-3-alkylthiazolinium bromide ( 2a ), a 1-(dichlorophosphino) substituted 1, 3-azaphospholo[5,1-b]thiazoline ( 4 ) was obtained. The chemical shift of the two-coordinate phosphorus in 1,3-azaphosphole derivatives clearly reflects the influence of the heterocyclic system annulated to its 1,5-bond and of the substituents in its 2-and 4-positions.     

Structure-mechanics statistical learning uncovers mechanical relay in proteins

A protein''s adaptive response to its substrates is one of the key questions driving molecular physics and physical chemistry. This work employs the recently developed structure-mechanics statistical learning method to establish a mechanical perspective. Specifically, by mapping all-atom molecular dynamics simulations onto the spring parameters of a backbone-side-chain elastic network model, the chemical moiety specific force constants (or mechanical rigidity) are used to assemble the rigidity graph, which is the matrix of inter-residue coupling strength. Using the S1A protease and the PDZ3 signaling domain as examples, chains of spatially contiguous residues are found to exhibit prominent changes in their mechanical rigidity upon substrate binding or dissociation. Such a mechanical-relay picture thus provides a mechanistic underpinning for conformational changes, long-range communication, and inter-domain allostery in both proteins, where the responsive mechanical hotspots are mostly residues having important biological functions or significant mutation sensitivity.

Protein residues exhibit specific routes of mechanical relay as the adaptive responses to substrate binding or dissociation. On such physically contiguous connections, residues experience prominent changes in their coupling strengths.