Fragment screening and structural analyses highlight the ATP-assisted ligand binding for inhibitor discovery against type 1 methionyl-tRNA synthetase.

Methionyl-tRNA synthetase (MetRS) charges tRNAMet with l-methionine (L-Met) to decode the ATG codon for protein translation, making it indispensable for all cellular lives. Many gram-positive bacteria use a type 1 MetRS (MetRS1), which is considered a promising antimicrobial drug target due to its low sequence identity with human cytosolic MetRS (HcMetRS, which belongs to MetRS2). Here, we report crystal structures of a representative MetRS1 from Staphylococcus aureus (SaMetRS) in its apo and substrate-binding forms. The connecting peptide (CP) domain of SaMetRS differs from HcMetRS in structural organization and dynamic movement. We screened 1049 chemical fragments against SaMetRS preincubated with or without substrate ATP, and ten hits were identified. Four cocrystal structures revealed that the fragments bound to either the L-Met binding site or an auxiliary pocket near the tRNA CCA end binding site of SaMetRS. Interestingly, fragment binding was enhanced by ATP in most cases, suggesting a potential ATP-assisted ligand binding mechanism in MetRS1. Moreover, co-binding with ATP was also observed in our cocrystal structure of SaMetRS with a class of newly reported inhibitors that simultaneously occupied the auxiliary pocket, tRNA site and L-Met site. Our findings will inspire the development of new MetRS1 inhibitors for fighting microbial infections.

Visible-Light-Driven Redox Neutral Direct C-H Amination of Glycine Derivatives and Peptides with N-Acyloxyphthalimides.

A room temperature, visible-light-promoted and redox neutral direct C-H amination of glycine and peptides has been firstly accomplished by using N-acyloxyphthalimide or -succinimide as nitrogen-radical precursor. The present strategy provides ways to introduce functionalities such as N-acyloxyphthalimide or -succinimide specifically to terminal glycine segment of peptides. Herein, mild conditions and high functional-group tolerance allow the preparation of non-natural α-amino acids and modification of corresponding peptides in this way.

Identification of new building blocks by fragment screening for discovering GyrB inhibitors.

DNA gyrase is an essential DNA topoisomerase that exists only in bacteria. Since novobiocin was withdrawn from the market, new scaffolds and new mechanistic GyrB inhibitors are urgently needed. In this study, we employed fragment screening and X-ray crystallography to identify new building blocks, as well as their binding mechanisms, to support the discovery of new GyrB inhibitors. In total, 84 of the 618 chemical fragments were shown to either thermally stabilize the ATPase domain of Escherichia coli GyrB or inhibit the ATPase activity of E. coli gyrase. Among them, the IC50 values of fragments 10 and 23 were determined to be 605.3 µM and 446.2 µM, respectively. Cocrystal structures of the GyrB ATPase domain with twelve fragment hits were successfully determined at a high resolution. All twelve fragments were deeply inserted in the pocket and formed H-bonds with Asp73 and Thr165, and six fragments formed an additional H-bond with the backbone oxygen of Val71. Fragment screening further highlighted the capability of Asp73, Thr165 and Val71 to bind chemicals and provided diverse building blocks for the design of GyrB inhibitors.

In-vitro and in-vivo comparison of T-OA microemulsions and solid dispersions based on EPDC.

The goal of this study was to enhance the absorption of a new water-insoluble antitumor lead compound, T-OA (3ß-hydroxyolea-12-en-28-oic acid-3, 5, 6-trimethylpyrazin-2-methyl ester). Early-stage preparation discovery concept (EPDC) was employed in this study. Based on this concept, a microemulsion system was chosen as the method of improving bioavailability. The solubility of T-OA was checked in different oils, surfactants and cosurfactants. Ternary phase diagrams were constructed to evaluate the microemulsion domain. Developed high-performance liquid chromatography method was used to determine drug content. The transparent o/w microemulsion formulation composed of oleic acid (oil), Tween 80 (surfactant), ethanol (co-surfactant) and water enhanced the solubility of T-OA up to 20 mg/mL. It was characterized in terms of appearance, content, viscosity, zeta potential, conductivity, morphology and particle size. The particle size distribution, viscosity, conductivity and zeta potential were found to be 70 nm, 15.57 MPa s, 44.1 µS cm(-1) and -0.174, respectively. Oral bioavailability of T-OA microemulsion and oleic acid solution were checked by using rat model. Contrast to the solid dispersion and proto drug, the area-under-the-curve (AUC) of T-OA microemulsion and oleic acid solution were significantly enhanced. The relative bioavailability of T-OA microemulsion was found to be 5654.7%, which is 57-fold higher than the pure drug. Improved T-OA solubility in microemulsion was found sustained 48 h in dilution study. While the solid dispersion may precipitate under the gastrointestinal circumstance based on dilution results. The in-vivo and in-vitro results indicated that, compare to improve the solubility, it is more important to maintain and prolong the T-OA dissolved status, for improvement of the in-vivo absorption.

Preparation and evaluation of solid dispersions of a new antitumor compound based on early-stage preparation discovery concept.

Ensuring sufficient drug solubility is a crucial problem in pharmaceutical-related research. For water-insoluble drugs, various formulation approaches are employed to enhance the solubility and bioavailability of lead compounds. The goal of this study was to enhance the dissolution and absorption of a new antitumor lead compound, T-OA. Early-stage preparation discovery concept was employed in this study. Based on this concept, a solid dispersion system was chosen as the method of improving drug solubility and bioavailability. Solid dispersions of T-OA in polyvinylpyrrolidone (PVP) K30 were prepared by the solvent evaporation method. Dissolution testing determined that the ideal drug-to-PVP ratio was 1:5. X-ray diffraction, Fourier transform infrared spectroscopy, and differential scanning calorimetry were employed to confirm the formation of solid dispersions. Scanning electron microscopy demonstrated that T-OA was converted into an amorphous form. Both in vitro dissolution testing and the in vivo studies demonstrated that the solubility and bioavailability of T-OA were significantly improved when formulated in a solid dispersion with PVP. The dissolution rate of the T-OA/PVP solid dispersion was greatly enhanced relative to the pure drug, and the relative bioavailability of T-OA solid dispersions was found to be 392.0%, which is 4-fold higher than the pure drug.

Multicomponent All-Carbon Cascade and Sequential Annulation: Construction of Functionalized Decalins.

The decalin skeleton is found in numerous bioactive molecules. The present study describes a multicomponent all-carbon cascade and sequential annulation involving benzoylacetonitrile derivatives and 2-arylidene-1,3-indanediones that yields highly functionalized decalin derivatives. The reaction strategy consisted of a consecutive Michael/Michael/tautomerization/Michael/Aldol annulation sequence and involved organic amine catalysts, mild conditions, and high stereoselectivity. This strategy, using a one-pot approach, resulted in the construction of four C-C bonds and the formation of fused carbocyclic decalin derivatives.

Design, Synthesis, and Proof-of-Concept of Triple-Site Inhibitors against Aminoacyl-tRNA Synthetases.

Aminoacyl-tRNA synthetases (aaRSs) are promising drug targets due to their essential roles in protein translation. Although current inhibitors primarily occupy one or two of the three substrate binding sites on aaRSs, we report here the structure-based design of the first class of triple-site aaRS inhibitors by targeting Salmonella enterica threonyl-tRNA synthetase (SeThrRS). Competition of our compounds with all three substrates on SeThrRS binding was confirmed via isothermal titration calorimetry assays. Cocrystal structures of three compounds bound to SeThrRS unambiguously confirmed their substrate-mimicking triple-site binding mode. Compound 36j exhibited the best enzyme activity against SeThrRS with IC50 = 19 nM and Kd = 35.4 nM. Compounds 36b, 36k, and 36l exhibited antibacterial activities with minimum inhibitory concentration values of 2-8 µg/mL against the tested bacteria, which are superior to those of the reported dual-site ThrRS inhibitors. Our study provides the first proof-of-concept for developing triple-site inhibitors against aaRSs, inspiring future aaRS-based drug discoveries.

Structure-Guided Design of Halofuginone Derivatives as ATP-Aided Inhibitors Against Bacterial Prolyl-tRNA Synthetase.

Aminoacyl-tRNA synthetases (aaRSs) are promising antimicrobial targets due to their essential roles in protein translation, and expanding their inhibitory mechanisms will provide new opportunities for drug discovery. We report here that halofuginone (HF), an herb-derived medicine, moderately inhibits prolyl-tRNA synthetases (ProRSs) from various pathogenic bacteria. A cocrystal structure of Staphylococcus aureus ProRS (SaProRS) with HF and an ATP analog was determined, which guided the design of new HF analogs. Compound 3 potently inhibited SaProRS at IC50 = 0.18 µM and Kd = 30.3 nM and showed antibacterial activities with an MIC of 1-4 µg/mL in vitro. The bacterial drug resistance to 3 only developed at a rate similar to or slower than those of clinically used antibiotics in vitro. Our study indicates that the scaffold and ATP-aided inhibitory mechanism of HF could apply to bacterial ProRS and also provides a chemical validation for using bacterial ProRS as an antibacterial target.

Structure-guided optimization and mechanistic study of a class of quinazolinone-threonine hybrids as antibacterial ThrRS inhibitors.

Aminoacyl-tRNA synthetases (aaRSs) are an attractive class of antibacterial drug targets due to their essential roles in protein translation. While most traditional aaRS inhibitors target the binding pockets of substrate amino acids and/or ATP, we recently developed a class of novel tRNA-amino acid dual-site inhibitors including inhibitor 3 ((2S,3R)-2-amino-N-((E)-4-(6,7-dichloro-4-oxoquinazolin-3(4H)-yl)but-2-en-1-yl)-3-hydroxybutanamide) against threonyl-tRNA synthetase (ThrRS). Here, the binding modes and structure-activity relationships (SARs) of these inhibitors were analyzed by the crystal structures of Salmonella enterica ThrRS (SeThrRS) in complex with three of them. Based on the cocrystal structures, twelve quinazolinone-threonine hybrids were designed and synthesized, and their affinities, enzymatic inhibitory activities, and cellular potencies were evaluated. The best derivative 8g achieved a Kd value of 0.40 µM, an IC50 value of 0.50 µM against SeThrRS and MIC values of 16-32 µg/mL against the tested bacterial strains. The cocrystal structure of the SeThrRS-8g complex revealed that 8g induced a bended conformation for Met332 by forming hydrophobic interactions, which better mimicked the binding of tRNAThr to ThrRS. Moreover, the inhibitory potency of 8g was less impaired than a reported ATP competitive inhibitor at high concentrations of ATP, supporting our hypothesis that tRNA site inhibitors are likely superior to ATP site inhibitors in vivo, where ATP typically reaches millimolar concentrations.

Photoactivatable Fluorogenic Labeling via Turn-On "Click-Like" Nitroso-Diene Bioorthogonal Reaction.

Fluorogenic labeling enables imaging cellular molecules of interest with minimal background. This process is accompanied with the notable increase of the quantum yield of fluorophore, thus minimizing the background signals from unactivated profluorophores. Herein, the development of a highly efficient and bioorthogonal nitroso-based Diels-Alder fluorogenic reaction is presented and its usefulness is validated as effective and controllable in fluorescent probes and live-cell labeling strategies for dynamic cellular imaging. It is demonstrated that nitroso-based cycloaddition is an efficient fluorogenic labeling tool through experiments of further UV-activatable fluorescent labeling on proteins and live cells. The ability of tuning the fluorescence of labeled proteins by UV-irradiation enables selective activation of proteins of interest in a particular cell compartment at a given time point, while leaving the remaining labeled molecules untouched.

[Chemical constituents of antibacterial activity fraction of Angelica polymorpha].

OBJECTIVE: To study chemical constituents of antibacterial activity fraction of Angelica polymorpha. METHODS: Compounds were isolated by repeatedly silica gel column chromatography and recrystallization. Their structures were identified by physical and chemical evidences and spectral methods. RESULTS: Seven compounds were obtained from the antibacterial activity fraction, their structures were elucidated as: bisabolangelone(I), isoimperatorin (II), oxypeucedanine(III), isooxypeucedanine(IV), oxypeucedanin hydrate(V), bergapten(VI), pabulenol(VII). CONCLUSION: Bisabolangelone(I) is obtained from this plant for the first time. Compound (II)-(VII) belong to linear furanocourmarins.

Direct ß-selectivity of α,ß-unsaturated γ-butyrolactam for asymmetric conjugate additions in an organocatalytic manner.

The ß-selective asymmetric addition of γ-butyrolactam with cyclic imino esters catalyzed by a bifunctional chiral tertiary amine has been developed, which provides an efficient access to optically active ß-position functionalized pyrrolidin-2-one derivatives in both high yield and enantioselectivity (up to 78% yield and 95 : 5 er). This is the first catalytic method to access chiral ß-functionalized pyrrolidin-2-one via a direct organocatalytic approach.

Highly diastereoselective oxa-[3+3] cyclization with C,N-cyclic azomethine imines via the copper-catalyzed aerobic oxygenated C[double bond, length as m-dash]C bond of indoles.

Herein, a copper-catalyzed highly diastereoselective aerobic oxygenated [3+3] cyclization of 3-substituted indoles with C,N-cyclic azomethine imines using oxygen as the sole oxidant under mild conditions has been developed. This protocol provides a simple and convenient approach for constructing [2,3]-fused indoline O-heterocycles bearing two pharmaceutically intriguing parts, tetrahydroisoquinoline and indoline. Good yields and excellent diastereoselectivity under mild reaction conditions were observed.

The anti-ulcer activities of bisabolangelone from Angelica polymorpha.

AIM OF THE STUDY: Evaluate the anti-ulcer effects of bisabolangelone from Angelica polymorpha Maxim and provide the basic data to further study for the Angelica polymorpha and bisabolangelone. MATERIALS AND METHODS: Bisabolangelone was isolated from Angelica polymorpha Maxim collected from Shennongjia Forest District of China. The structure of bisabolangelone was elucidated by NMR and MS spectrums. The anti-ulcer effects were evaluated with length of lesion (mm) and activity of H(+)/K(+)-ATPase in two models induced by ethanol and Pylorus ligation. Experimental groups were administered with different doses of bisabolangelone (3.8, 7.6 and 15.3 mg/kg). The positive control group was administered omeprazole with a dose of 3.3 mg/kg. RESULTS: Bisabolangelone significantly reduced the length of lesion (3.8, 7.6 and 15.3 mg/kg, P<0.01), inhibited the activity of H(+)/K(+)-ATPase (3.8, 7.6 and 15.3 mg/kg, P<0.01), decreased the volume of gastric juice (7.6 and 15.3 mg/kg, P<0.05), and increased the pH value of gastric juice (7.6 and 15.3 mg/kg, P<0.01, 3.8 mg/kg, P<0.05). CONCLUSIONS: Bisabolangelone is the main anti-ulcer active compound of Angelica polymorpha, and remarkably preventive and therapeutic action on gastric ulcer. It is possible that bisabolangelone inhibited the activity of the H(+)/K(+)-ATPase, then reducing the secretion of H(+), and the anti-ulcer mechanism of bisabolangelone was deserved to be further studied.