Synthesis of 2H-pyrroles via the 1,3-dipolar cycloaddition reaction of nitrile ylides with acrylamides

3,4-Dihydro-2H-pyrrole derivatives were synthesized by the 1,3-dipolar cycloaddition reaction of nitrile ylides with acrylamides. Acrylamide substitution patterns and benzimidoyl chloride equilibration were investigated.     

Identification of flavonoids using liquid chromatography with electrospray ionization and ion trap tandem mass spectrometry with an MS/MS library

Searchable MS/MS spectra libraries, constructed using the results of liquid chromatography coupled with electrospray ionization (ESI) tandem mass spectrometry (LC/MS/MS) with data-dependent acquisition on an ion trap mass spectrometer, are presented with regard to the identification and confirmation of a variety of closely related flavonoids in a set of biological samples. Flavonoids were found to exhibit a maximum amount of structurally specific MS/MS spectra at 45% of normalized collision energy on the instrument used, without wideband activation. These MS/MS spectra were then searched automatically against a 297-substance MS/MS library that contains many previously acquired spectra of standard flavonoids. The possible applications of this powerful technique to biological samples are also discussed. Daidzein and genistein were identified through the MS/MS spectra library while searching through LC/MS/MS data for plant and microbial extracts. Moreover, these compounds proved completely distinguishable from other flavonoids of closely related structures in the MS/MS spectra library, using the NIST MS search program. The applicability of the library-searchable spectra at low concentrations was demonstrated by successful identification of daidzein and genistein at 0.05 and 0.5 microg/mL, respectively.     

Peptide microarrays for the determination of protease substrate specificity

A method is described for the preparation of substrate microarrays that allow for the rapid determination of protease substrate specificity. Peptidyl coumarin substrates, synthesized on solid support using standard techniques, are printed onto glass slides using DNA microarraying equipment. The linkage from the peptide to the slide is formed through a chemoselective reaction, resulting in an array of uniformly displayed fluorogenic substrates. The arrays can be treated with proteases to yield substrate specificity profiles. Standard instrumentation for visualization of microarrays can be used to obtain comparisons of the specificity constants for all of the prepared substrates. The utility of these arrays is demonstrated by the selective cleavage of preferred substrates with trypsin, thrombin, and granzyme B, and by assessing the extended substrate specificity of thrombin using a microarray of 361 different peptidyl coumarin substrates.     

New Acetylcholinesterase‐Inhibitory Pregnane Glycosides of Cynanchum atratum Roots

Three new pregnane glycosides, cynatroside A ( 1 ), cynatroside B ( 2 ), and cynatroside C ( 3 ), isolated from the roots of Cynanchum atratum (Asclepiadaceae), were characterized as 7β‐{[O‐α‐L ‐cymaropyranosyl‐(1→4)‐O‐β‐D ‐digitoxopyranosyl‐(1→4)‐β‐D ‐oleandropyranosyl]oxy}‐3,4,4a,4b,5,6,7,8,10,10a‐decahydro‐6α‐hydroxy‐4b‐ methyl‐2‐(2‐methyl‐3‐furyl)phenanthren‐1(2H)‐one ( 1 ), 7β‐{[O‐β‐D ‐cymaropyranosyl‐(1→4)‐O‐α‐L ‐diginopyranosyl‐(1→4)‐β‐D ‐cymaropyranosyl]oxy}‐3,4,4a,4b,5,6,7,8,10,10a‐decahydro‐2,6α‐dihydroxy‐4b‐methyl‐2‐(2‐methyl‐3‐furyl)phenanthren‐1(2H)‐one ( 2 ), and 7β‐{[O‐α‐L ‐cymaropyranosyl‐(1→4)‐O‐β‐D ‐digitoxopyranosyl‐(1→4)‐β‐L ‐cymaropyranosyl]oxy}‐3,4,4a,4b,5,6,7,8,10,10a‐decahydro‐2,6α‐dihydroxy‐4b‐methyl‐2‐(2‐methyl‐3‐furyl)phenanthren‐1(2H)‐one ( 3 ), respectively. In addition, ten known constituents were identified, i.e., cynascyroside D ( 4 ), glaucoside C ( 5 ), glaucoside D ( 6 ), atratoside A ( 7 ), 2,4‐dihydroxyacetophenone ( 8 ), 4‐hydroxyacetophenone ( 9 ), syringic acid ( 10 ), azelaic acid ( 11 ), suberic acid ( 12 ), and succinic acid ( 13 ). Among these compounds, 1 – 4 significantly inhibit acetylcholinesterase activity.     

Can an in silico drug-target search method be used to probe potential mechanisms of medicinal plant ingredients?

Medicinal plants have been explored therapeutically in traditional medicines and are a valuable source for drug discovery. Insufficient knowledge about the molecular mechanism of these medicinal plants limits the scope of their application and hinders the effort to design new drugs using the therapeutic principles of herbal medicines. This problem can be partially alleviated if efficient methods for rapid identification of protein targets of herbal ingredients can be introduced. Efforts have been directed at developing efficient computer methods for facilitating target identification. Various methods being explored or under investigation are reviewed here. So far, one computer method, INVDOCK, has been specifically used for automated drug target identification. Its usefulness in the identification of therapeutic targets of medicinal herbal ingredients as well as synthetic chemicals is reviewed. The majority of INVDOCK identified therapeutic targets of several well-known medicinal herbal ingredients have been found to be confirmed or implicated by experiments, which suggests the potential of in silico methods in facilitating the study of molecular mechanism of medicinal plants.     

Heterocyclic Substitutions Greatly Improve Affinity and Stability of Folic Acid towards FRα. an In Silico Insight

Folate receptor alpha (FRα) is known as a biological marker for many cancers due to its overexpression in cancerous epithelial tissue. The folic acid (FA) binding affinity to the FRα active site provides a basis for designing more specific targets for FRα. Heterocyclic rings have been shown to interact with many receptors and are important to the metabolism and biological processes within the body. Nineteen FA analogs with substitution with various heterocyclic rings were designed to have higher affinity toward FRα. Molecular docking was used to study the binding affinity of designed analogs compared to FA, methotrexate (MTX), and pemetrexed (PTX). Out of 19 FA analogs, analogs with a tetrazole ring (FOL03) and benzothiophene ring (FOL08) showed the most negative binding energy and were able to interact with ASP81 and SER174 through hydrogen bonds and hydrophobic interactions with amino acids of the active site. Hence, 100 ns molecular dynamics (MD) simulations were carried out for FOL03, FOL08 compared to FA, MTX, and PTX. The root mean square deviation (RMSD) and root mean square fluctuation (RMSF) of FOL03 and FOL08 showed an apparent convergence similar to that of FA, and both of them entered the binding pocket (active site) from the pteridine part, while the glutamic part was stuck at the FRα pocket entrance during the MD simulations. Molecular mechanics Poisson-Boltzmann surface accessible (MM-PBSA) and H-bond analysis revealed that FOL03 and FOL08 created more negative free binding and electrostatic energy compared to FA and PTX, and both formed stronger H-bond interactions with ASP81 than FA with excellent H-bond profiles that led them to become bound tightly in the pocket. In addition, pocket volume calculations showed that the volumes of active site for FOL03 and FOL08 inside the FRα pocket were smaller than the FA–FRα system, indicating strong interactions between the protein active site residues with these new FA analogs compared to FA during the MD simulations.     

Diastereoselective diaza-Cope rearrangement reaction

Steric effect is used to obtain a highly diastereoselective rearrangement reaction.     

Direct Catalytic Asymmetric Mannich Reaction with Dithiomalonates as Excellent Mannich Donors: Organocatalytic Synthesis of (R)‐Sitagliptin

In this study, dithiomalonates (DTMs) were demonstrated to be exceptionally efficient Mannich donors in terms of reactivity and stereoselectivity in cinchona‐based‐squaramide‐catalyzed enantioselective Mannich reactions of diverse imines or α‐amidosulfones as imine surrogates. Owing to the superior reactivity of DTMs as compared to conventional malonates, the catalyst loading could be reduced to 0.1 mol % without the erosion of enantioselectivity (up to 99 % ee). Furthermore, by the use of a DTM, even some highly challenging primary alkyl α‐amidosulfones were smoothly converted into the desired adducts with excellent enantioselectivity (up to 97 % ee), whereas the use of a malonate or monothiomalonate resulted in no reaction under identical conditions. The synthetic utility of the chiral Mannich adducts obtained from primary alkyl substrates was highlighted by the organocatalytic, coupling‐reagent‐free synthesis of the antidiabetic drug (?)‐(R)‐sitagliptin.