Polyphyllin D Shows Anticancer Effect through a Selective Inhibition of Src Homology Region 2-Containing Protein Tyrosine Phosphatase-2 (SHP2)

Natural products have continued to offer tremendous opportunities for drug development, as they have long been used in traditional medicinal systems. SHP2 has served as an anticancer target. To identify novel SHP2 inhibitors with potential anticancer activity, we screened a library containing 658 natural products. Polyphyllin D was found to selectively inhibit SHP2 over SHP1, whereas two other identified compounds (echinocystic acid and oleanolic acid) demonstrated dual SHP1 and SHP2 inhibition. In a cell-based assay, polyphyllin D exhibited cytotoxicity in Jurkat cells, an acute lymphoma leukemia cell line, whereas the other two compounds were ineffective. Polyphyllin D also decreased the level of phosphorylated extracellular signal-regulated kinase (p-ERK), a proliferation marker in Jurkat cells. Furthermore, knockdown of protein tyrosine phosphatase (PTP)N6 (SHP1) or PTPN11 (SHP2) decreased p-ERK levels. However, concurrent knockdown of PTPN6 and PTPN11 in Jurkat cells recovered p-ERK levels. These results demonstrated that polyphyllin D has potential anticancer activity, which can be attributed to its selective inhibition of SHP2 over SHP1.     

Studies on molecular mechanism between SHP2 and pyridine derivatives by 3D-QSAR,molecular docking and MD simulations

BackgroundSrc homology 2 (SH2)-containing protein tyrosine phosphatase 2 (SHP2) as a major phosphatase would affect the development of tumors by regulating several cellular processes, and is a significant potential target for cancer treatment.MethodsIn the present work, a series of pyridine derivatives possessing a wide range of inhibitory activity was employed to investigate the structural requirements by developing three dimensional quantitative structure–activity relationship (3D-QSAR) models using comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) methods. The results show that CoMFA (R²_cv = 0.646, R²_pred = 0.5587) and CoMSIA (R²_cv = 0.777, R²_pred = 0.7131) have excellent stability and predictability. The relationship between the inhibitory activity and structure of the inhibitors was analyzed by the derived contour maps. Furthermore, the QSAR models were validated by molecular docking and molecular dynamics simulations, which were also applied to reveal the potential molecular mechanism of these inhibitors.FindingsIt was found that Arg110, Asn216, Thr218, Thr252 and Pro490 play a crucial role in stabilizing the inhibitors. Additionally, MM/PBSA calculations provided the binding free energy were also conducted to explain the discrepancy of binding activities. Overall, the outcomes of this work could provide useful information and theoretical guidance for the development of novel and potent SHP2 inhibitors.     

Exploring the reason for increased activity of SHP2 caused by D61Y mutation through molecular dynamics

Juvenile myelomonocytic leukaemia, an aggressive myeloproliferative neoplasm, is characterized by thrombocytopenia, splenomegaly, fever and excess myelomonocytic cells. Approximately 35% of patients with JMML occur D61Y mutation in PTPN11, and it increases the activity of the protein. However, the effect of the D61Y mutation on SHP2 conformations in molecular basis is poorly understood. Therefore, the molecular dynamics simulations on SHP2-D61Y and SHP2-WT were performed to explore the effect of D61Y mutation on SHP2 and explain the reason for high activity of SHP2-D61Y mutant. The study on the RMSF, per-residue RMSD, PCA, DCCM and secondary structure found that the flexibilities of regions (residues His458-Ser460 and Gln506-Ala509) in SHP2-D61Y were higher than the corresponding regions in SHP2-WT, and the conformations of these regions almost transformed from α-helix and β-strand to Turn, respectively. Thus, the catalytical sites in the PTP domain (residues Asn217-Thr524) were exposed to the substrate easily, which contributed to the enhancement of SHP2-D61Y activity. Moreover, the residue interaction network, H bond occupancy and binding free energy were calculated, revealing that conformational difference were caused by distinctions in residue-residue interactions between Asp/Tyr61-Gln506, Gln506-Gln510, Gln506-Phe251, Gln506-Gly60, Gln506-Tyr63, Asp/Tyr61-Cys459, Cys459-Ile463 and Cys459-Arg465. The study here may offer the valuable information to explore the reason for the increased activity of SHP2 after D61Y-mutation.     

Functional characterization of ttnI completing the tailoring steps for tautomycetin biosynthesis in Streptomyces griseochromogenes

The tautomycetin (TTN) biosynthetic gene cluster has been recently cloned and sequenced from Streptomyces griseochromogenes, unveiling four genes, ttnCDFI, as candidates to encode the tailoring steps for TTN biosynthesis. It is reported that (i) TtnC plays no essential role in TTN biosynthesis, (ii) TtnI catalyzes C-5 oxidation, and (iii) combining the previous findings with TtnFD, the tailoring steps from TTN F-1 to TTN take place in the order of TtnF-catalyzed C-1"/C-2" dehydration, TtnD-catalyzed C-3" decarboxylation, and TtnI-catalyzed C-5 oxidation.     

Synthesis and photophysical properties of 2,5,8,11‐tetrakis(5‐hexylthiophen‐2‐yl)tetrathieno[2,3‐a:3′,2′‐c:2′′,3′′‐f:3′′′,2′′′‐h]naphthalene

The title compound, C₅₈H₆₄S₈, has been prepared by Pd‐catalysed direct C—H arylation of tetrathienonaphthalene (TTN) with 5‐hexyl‐2‐iodothiophene and recrystallized by slow evaporation from dichloromethane. The crystal structure shows a completely planar geometry of the TTN core, crystallizing in the monoclinic space group P2₁/c. The structure consists of slipped π‐stacks and the interfacial distance between the mean planes of the TTN cores is 3.456 (5) Å, which is slightly larger than that of the comparable derivative of tetrathienoanthracene (TTA) with 2‐hexylthiophene groups. The packing in the two structures is greatly influenced by both the aromatic core of the structure and the alkyl side chains.     

Orphan nuclear receptor small heterodimer partner inhibits angiotensin II-stimulated PAI-1 expression in vascular smooth muscle cells

Angiotensin II is a major effector molecule in the development of cardiovascular disease. In vascular smooth muscle cells (VSMCs), angiotensin II promotes cellular proliferation and extracellular matrix accumulation through the upregulation of plasminogen activator inhibitor-1 (PAI-1) expression. Previously, we demonstrated that small heterodimer partner (SHP) represses PAI-1 expression in the liver through the inhibition of TGF-β signaling pathways. Here, we investigated whether SHP inhibited angiotensin II-stimulated PAI-1 expression in VSMCs. Adenovirus-mediated overexpression of SHP (Ad-SHP) in VSMCs inhibited angiotensin II- and TGF-β-stimulated PAI-1 expression. Ad-SHP also inhibited angiotensin II-, TGF-β- and Smad3-stimulated PAI-1 promoter activity, and angiotensin II-stimulated AP-1 activity. The level of PAI-1 expression was significantly higher in VSMCs of SHP^-/- mice than wild type mice. Moreover, loss of SHP increased PAI-1 mRNA expression after angiotensin II treatment. These results suggest that SHP inhibits PAI-1 expression in VSMCs through the suppression of TGF-β/Smad3 and AP-1 activity. Thus, agents that target the induction of SHP expression in VSMCs might help prevent the development and progression of atherosclerosis.     

Study of interfacial chemistry on direct curing adhesion between Ni–P plating and rubber using 1,3,5‐triazine‐2,4,6‐trithiol monosodium salt

Direct adhesion between Ni–P‐plated iron and acrylonitrile–butadiene rubber, hydrogenated acrylonitrile–butadiene rubber and ethylene–propylene rubber was successful using 1,3,5‐triazine‐2,4,6‐trithiol monosodium salt (TTN) without any adhesive. Peel strength in the adherends was influenced by the amount of TTN employed. The interfacial structure between Ni–P‐plated iron and curing rubbers has been investigated with x‐ray microanalysis, x‐ray photoelectron spectroscopy and scanning electron microscopy. The TTN derivatives gathered locally at the interface between the Ni–P‐plated iron and curing rubber adherends. The TTN layer located near the interface is referred to as a reinforcement layer. This layer was in general ～70 nm thick and consisted of composites of the Ni salt of TTN. The TTN is thought to work as a binder that bonds between Ni–P‐plated iron and rubber chains. The single bonds between both Ni–P‐plated iron and rubber TTN was confirmed from Kraus plots and model experiments using TTN. Copyright © 2003 John Wiley & Sons, Ltd.     

Reaction of 3-Alkenols with Thallium Trinitrate: An Unexpected and Useful Ring Contraction

The first thallium trinitrate (TTN) mediated ring contraction of cyclic homoallylic alcohols, using a 1:1 mixture of AcOH and H₂O as solvent, is described. The reaction of two of these alcohols with excess of TTN in pentane gave α-spirocyclopentyl-γ-butirolactones in reasonable yields.     

A Formylglycine-Peptide for the Site-Directed Identification of Phosphotyrosine-Mimetic Fragments**

Discovery of protein-binding fragments for precisely defined binding sites is an unmet challenge to date. Herein, formylglycine is investigated as a molecular probe for the sensitive detection of fragments binding to a spatially defined protein site . Formylglycine peptide 3 was derived from a phosphotyrosine-containing peptide substrate of protein tyrosine phosphatase PTP1B by replacing the phosphorylated amino acid with the reactive electrophile. Fragment ligation with formylglycine occurred in situ in aqueous physiological buffer. Structures and kinetics were validated by NMR spectroscopy. Screening and hit validation revealed fluorinated and non-fluorinated hit fragments being able to replace the native phosphotyrosine residue. The formylglycine probe identified low-affinity fragments with high spatial resolution as substantiated by molecular modelling. The best fragment hit, 4-amino-phenyl-acetic acid, was converted into a cellularly active, nanomolar inhibitor of the protein tyrosine phosphatase SHP2.     

Exploring the Distinct Binding and Activation Mechanisms for Different CagA Oncoproteins and SHP2 by Molecular Dynamics Simulations

CagA is a major virulence factor of Helicobacter pylori. H. pylori CagA is geographically subclassified into East Asian CagA and Western CagA, which are characterized by the presence of a EPIYA-D or EPIYA-C segment. The East Asian CagA is more closely associated with gastric cancer than the Western CagA. In this study, molecular dynamic (MD) simulations were performed to investigate the binding details of SHP2 and EPIYA segments, and to explore the allosteric regulation mechanism of SHP2. Our results show that the EPIYA-D has a stronger binding affinity to the N-SH2 domain of SHP2 than EPIYA-C. In addition, a single EPIYA-D binding to N-SH2 domain of SHP2 can cause a deflection of the key helix B, and the deflected helix B could squeeze the N-SH2 and PTP domains to break the autoinhibition pocket of SHP2. However, a single EPIYA-C binding to the N-SH2 domain of SHP2 cannot break the autoinhibition of SHP2 because the secondary structure of the key helix B is destroyed. However, the tandem EPIYA-C not only increases its binding affinity to SHP2, but also does not significantly break the secondary structure of the key helix B. Our study can help us better understand the mechanism of gastric cancer caused by Helicobacter pylori infection.     

Thallium trinitrate mediated oxidation of 3-alkenols: ring contraction vs cyclization

The reaction of a series of six-membered ring 3-alkenols with thallium trinitrate (TTN) in three different experimental conditions was studied. Either cyclization products or ring contraction products were obtained, depending on the structure of the substrate as well as the nature of the solvent. The reaction of a seven-membered ring 3-alkenol with TTN led to the ring contraction product exclusively.     

Stereoselective synthesis of d- and L-carbocyclic nucleosides by enzymatically catalyzed kinetic resolution

An efficient synthesis of (S)- or (R)-3-(benzyloxy-methyl)-cyclopent-3-enol was developed by appling an enzyme-catalyzed kinetic-resolution approach. This procedure allowed the syntheses of the enantiomeric building blocks (S)- and (R)-cyclopentenol with high optical purity (>98?% ee). In contrast to previous approaches, the key advantage of this procedure is that the resolution is done on the level of enantiomers that only contain one stereogenic center. Owing to this feature, it was possible to chemically convert the enantiomers into each other. By using this route, the starting materials for the syntheses of carbocyclic D- and L-nucleoside analogues were readily accessible. 3',4'-Unsaturated D- or L-carbocyclic nucleosides were obtained from the condensation of various nucleobases with (S)- or (R)-cyclopentenol. Functionalization of the double bond in 3'-deoxy-3',4'-didehydro-carba-D-thymidine led to a variety of new nucleoside analogues. By using the cycloSal approach, their corresponding phosphorylated metabolites were readily accessable. Moreover, a new synthetic route to carbocyclic 2'-deoxy-nucleosides was developed, thereby leading to D- and L-carba-dT. D-Carba-dT was tested for antiviral activity against multidrug-resistance HIV-1 strain E2-2 and compared to the known antiviral agent d4T, as well as L-carba-dT. Whilst L-carba-dT was found to be inactive, its D-analogue showed remarkably high activity against the resistant virus and significantly better than that of d4T. However, against the wild-type virus strain NL4/3, d4T was found to be more-active than D-carba-dT.     

Structure, reactivity and solution behaviour of [Re(ser)(7-MeG)(CO)(3)] and [Re(ser)(3-pic)(CO)(3)]: "nucleoside-mimicking" complexes based on the fac-[Re(CO)(3)](+) moiety

The fac-[Re(CO)(3)](+) moiety was reacted with the amino acid serine (D- and L-ser) and with 7-methylguanine (7-MeG), 3-methylpyridine (3-pic) or adenine (ade) to yield novel complexes intended as nucleoside-mimicking compounds. Reaction of [Re(H(2)O)(3)(CO)(3)](+)(1) with L-ser yields the complex [Re(L-ser)(2)(CO)(3)](L-2). X-Ray structure analysis of L-2 reveals that one of the two amino acids is bound to the metal centre in a bidentate fashion while the other amino acid is bound as a zwitterion via the carboxylate oxygen only. Reaction of L-2 and of [Re(D-ser)(2)(CO)(3)](D-2) with 7-MeG yields complexes [Re(L-ser)(7-MeG)(CO)(3)](L-3) and [Re(D-ser)(7-MeG)(CO)(3)](D-3) respectively. Complexes L-3 and D-3 are received as a mixture of diastereomers. If 3-pic is used instead of 7-MeG complex [Re(L-ser)(3-pic)(CO)(3)](L-4) is obtained in good yield, while interaction of L-2 with ade gives a mixture of five distinct species. Crystallization gave one single diastereomer for L-3 and D-3 and the two forms for 4 respectively. X-Ray structure analyses reveal that in all cases the amino acid is bound in a chelate fashion with the base occupying the sixth co-ordination site. When crystals of either 2 or 3 are dissolved in a CD(3)OD/D(2)O mixture (1:1, 293 K) rapid transformation to the diastereomeric mixture is observed. While for L-2 this reorganisation is fast on the NMR time scale even at 193 K, the rate constant for the rearrangement of L-3 and D-3 is 1.36 +/- 0.24 x 10(-2) s(-1) at 293 K.     

Synthesis of D- and L-selenomethionine double-labeled with deuterium and selenium-82

The synthesis of D- and L-selenomethionine labeled with ?2Se and three deuteriums at Se-methyl group (D- and L-[2H?, ?2Se]selenomethionine) was described. D- And L-[2H?, ?2Se]selenomethionine were prepared by condensation of (R)- and (S)-2-amino-4-bromobutylic acid with lithium [2H?, ?2Se]methaneselenolate, which was prepared from metal (82)Se and [2H?]methyl iodide. The optical purities of D- and L-[2H?, ?2Se]selenomethionine were determined by HPLC with a chiral stationary phase column and were found more than 99% ee. The chemical ionization mass spectra showed that the molecular related ion for N-isobutyloxycarbonyl ethyl ester derivatives of [2H?, ?2Se]selenomethionine did not overlap with the m/z values known from that of non-labeled selenomethionine.     

CYP505E3: A Novel Self‐Sufficient ω‐7 In‐Chain Hydroxylase

The self‐sufficient cytochrome P450 monooxygenase CYP505E3 from Aspergillus terreus catalyzes the regioselective in‐chain hydroxylation of alkanes, fatty alcohols, and fatty acids at the ω‐7 position. It is the first reported P450 to give regioselective in‐chain ω‐7 hydroxylation of C10–C16 n‐alkanes, thereby enabling the one step biocatalytic synthesis of rare alcohols such as 5‐dodecanol and 7‐tetradecanol. It shows more than 70 % regioselectivity for the eighth carbon from one methyl terminus, and displays remarkably high activity towards decane (TTN≈8000) and dodecane (TTN≈2000). CYP505E3 can be used to synthesize the high‐value flavour compound δ‐dodecalactone via two routes: 1) conversion of dodecanoic acid into 5‐hydroxydodecanoic acid (24 % regioselectivity), which at low pH lactonises to δ‐dodecalactone, and 2) conversion of 1‐dodecanol into 1,5‐dodecanediol (55 % regioselectivity), which can be converted into δ‐dodecalactone by horse liver alcohol dehydrogenase.     

Isolation, structural elucidation, and synthesis of RA-XVII, a novel bicyclic hexapeptide from Rubia cordifolia, and the effect of side chain at residue 1 upon the conformation and cytotoxic activity

A novel antitumor bicyclic hexapeptide RA-XVII was isolated from the roots of Rubia cordifolia. By spectral studies and synthetic approach, its structure was determined to be [D-2-aminobutyric acid-1]deoxybouvardin. Studies on the effect of side chain at residue 1 on cytotoxic activity and conformation showed that although it had little effect on the conformation of the molecule, it decreased the activity as it grew longer.     

Fluorescent probes for cytochrome p450 structural characterization and inhibitor screening

We have synthesized two luminescent probes (D-4-Ad and D-8-Ad) that target cytochrome P450cam. D-4-Ad luminescence is quenched by F?rster energy transfer upon binding (Kd = 0.83 muM) but is restored when the probe is displaced from the active site by camphor. In contrast, D-8-Ad (Kd approximately 0.02 muM) is not displaced from the enzyme, even in the presence of a large excess of camphor. The 2.2 A resolution crystal structure of the D-8-Ad:P450cam complex reveals extensive hydrophobic contacts between the probe and the enzyme, which result from the conformational flexibility of the B', F, and G helices. Probes with properties similar to those of D-4-Ad potentially could be useful for screening P450 inhibitors.     

CYP505E3: A Novel Self-Sufficient ω-7 In-Chain Hydroxylase

The self-sufficient cytochrome P450 monooxygenase CYP505E3 from Aspergillus terreus catalyzes the regioselective in-chain hydroxylation of alkanes, fatty alcohols, and fatty acids at the ω-7 position. It is the first reported P450 to give regioselective in-chain ω-7 hydroxylation of C10–C16 n-alkanes, thereby enabling the one step biocatalytic synthesis of rare alcohols such as 5-dodecanol and 7-tetradecanol. It shows more than 70 % regioselectivity for the eighth carbon from one methyl terminus, and displays remarkably high activity towards decane (TTN≈8000) and dodecane (TTN≈2000). CYP505E3 can be used to synthesize the high-value flavour compound δ-dodecalactone via two routes: 1) conversion of dodecanoic acid into 5-hydroxydodecanoic acid (24 % regioselectivity), which at low pH lactonises to δ-dodecalactone, and 2) conversion of 1-dodecanol into 1,5-dodecanediol (55 % regioselectivity), which can be converted into δ-dodecalactone by horse liver alcohol dehydrogenase.