Peptide stapling with the retention of double native side-chains

All-hydrocarbon stapling strategy has been widely applied for enhancing the proteolytic stability of peptides. However, two major technical hurdles to some extent limit the development of stapled peptides for therapeutic usage: rational selection of the stapling sites and the corresponding deletion of the native side chains. Previously we described the development of the olefin-terminated amino acids with the retention of native side chains and successfully applied them in the synthesis of hydrocarbon stapled peptides with single side-chain retention. Here, we explored the feasibility and effectiveness of hydrocarbon stapling strategy characterized as double side-chains retention. Modeled after a lengthy human immunodeficiency virus-1 (HIV-1) fusion inhibitor SC34EK, Leuⁱ, Serⁱ⁺⁴ and Lysⁱ, Leuⁱ⁺⁴ stapled peptides with the retention of double side-chains were effectively obtained. Our complementary study provided a convenient alternative to address where to install the staple in sequence for conventional all-hydrocarbon peptide stapling. Furthermore, this method not only conferred conformational reinforcement for SC34EK with high α-helicity and protease resistance, but also preserved the structural characteristic (key peripheral residues, charge and solubility) of the linear peptide to the maximum, which are crucial for anti-HIV-1 activity.     

Rational design of proteolytically stable, cell-permeable Peptide-based selective mcl-1 inhibitors

Direct chemical modifications provide a simple and effective means to "translate" bioactive helical peptides into potential therapeutics targeting intracellular protein-protein interactions. We previously showed that distance-matching bisaryl cross-linkers can reinforce peptide helices containing two cysteines at the i and i+7 positions and confer cell permeability to the cross-linked peptides. Here we report the first crystal structure of a biphenyl-cross-linked Noxa peptide in complex with its target Mcl-1 at 2.0 ? resolution. Guided by this structure, we remodeled the surface of this cross-linked peptide through side-chain substitution and N-methylation and obtained a pair of cross-linked peptides with substantially increased helicity, cell permeability, proteolytic stability, and cell-killing activity in Mcl-1-overexpressing U937 cells.     

Application of Snyder–Dolan classification scheme to the selection of “orthogonal” columns for fast screening of illicit drugs and impurity profiling of pharmaceuticals – I. Isocratic elution

Fourteen judiciously selected reversed phase columns were tested with 18 cationic drug solutes under the isocratic elution conditions advised in the Snyder–Dolan (S–D) hydrophobic subtraction method of column classification. The standard errors (S.E.) of the least squares regressions of log k′ vs. log k′_REF were obtained for a given column against a reference column and used to compare and classify columns based on their selectivity. The results are consistent with those obtained with a study of the 16 test solutes recommended by Snyder and Dolan. To the extent these drugs are representative, these results show that the S–D classification scheme is also generally applicable to pharmaceuticals under isocratic conditions. That is, those columns judged to be similar based on the 16 S–D solutes were similar based on the 18 drugs; furthermore those columns judged to have significantly different selectivities based on the 16 S–D probes appeared to be quite different for the drugs as well. Given that the S–D method has been used to classify more than 400 different types of reversed phases the extension to cationic drugs is a significant finding.     

Achieving cell penetration with distance-matching cysteine cross-linkers: a facile route to cell-permeable peptide dual inhibitors of Mdm2/Mdmx

We report the design of bisarylmethylene bromides as a new class of rigid, distance-matching cysteine cross-linkers. By cross-linking a peptide dual inhibitor of Mdm2/Mdmx containing cysteines at i,i+7 positions, dramatic enhancement in cell permeability was achieved, along with increased helicity and biological activity.     

A Peptide Stapling Strategy with Built-In Fluorescence by Direct Late-Stage C(sp2)−H Olefination of Tryptophan

Fluorescent stapled peptides are important chemical tools for detecting intracellular distribution, protein–protein interactions, and localization of target proteins. These peptides are usually labeled with bulky sized fluorophores through reactive functional groups, which may alter the physical properties and biological activities of peptides. Herein, a unique strategy is developed for synthesizing new stapled peptides with built-in fluorescence. The stapled peptides were prepared through Rh-catalyzed C(sp²)−H olefination in tryptophan (Trp) residues by using pyridine/pyrimidine as the directing groups under mild conditions. This method displays good regioselectivity and high efficiency. Furthermore, as a proof of concept for its biological applications, stapled peptides without additional fluorophore 9 a and 9 b were constructed for a cell imaging study. These peptides displayed strong binding affinity toward integrin αvβ3 in A549 cells by cell imaging experiments. Notably they demonstrated even better anticancer activity than commercial antagonist cyclic (RGDfK). The method will provide robust tools for the peptide macrocyclization field.     

Modeling the phase equilibria of hydrogen sulfide and carbon dioxide in mixture with hydrocarbons and water using the PCP-SAFT equation of state

The perturbed-chain polar statistical associating fluid theory (PCP-SAFT) equation of state is applied to correlate phase equilibria for mixtures of hydrogen sulfide (H₂S) and carbon dioxide (CO₂) with alkanes, with aromatics, and with water over wide temperature and pressure ranges. The binary mixtures of H₂S–methane and CO₂–methane are studied in detail including vapor–liquid, liquid–liquid and fluid–solid phase equilibria. Very satisfying results were obtained for the binary mixtures as well as for the ternary mixture of H₂S–CO₂–methane using the (constant) interaction parameters of the binary pairs.     

Structural modification and antitumor activity of antimicrobial peptide HYL

HYL derived from the venom of the solitary bee Hylaeus signatus (Hymenoptera: Colletidae) is an α-helical antimicrobial peptide with 16 residues. To explore whether HYL can be applied in anti-tumor therapy, we synthesized HYL and further modified its structure by using a solid-phase synthesis method, and then evaluated their antitumor activities. Firstly, we identified the key residues of HYL by alanine scanning strategy, and then a series of stapled peptides were synthesized by hydrocarbon stapling strategy without destroying the key residues. All the stapled peptides of HYL showed significant improvement not only in α-helicity, but also in antitumor activity and protease resistance when compared to the parent peptide HYL. The results showed that hydrophobicity and amphiphilicity are important factors affecting the antitumor activity of HYL, and the stapling strategy can significantly affect the proteolytic stability and helicity of HYL. What's more, we find that the stapled peptides HYL-14, HYL-16 and HYL-18 show a promising prospect for novel anti-tumor drug development.     

Design of stapled oxyntomodulin analogs containing functionalized biphenyl cross-linkers

A panel of three lipid-modified, functionalized biphenyl cross-linkers (fBph) were synthesized and subsequently employed in the preparation of the stapled oxyntomodulin (OXM) analogs. In a luciferase-based reporter assay, these stapled OXM analogs showed varying degree of potency in activating GLP-1R and GCGR, presumably due to the disparate effect of the lipid chains on the local environment close to the ligand-receptor binding interface. In particular, the fBph-1 cross-linked peptide with the lipid chain attached to position-3 of the biphenyl cross-linker exhibited the highest dual agonist activity.     

Influence of X-ray tube spectral distribution on uncertainty of calculated fluorescent radiation intensity

The relative radiation intensity (R_i) defined as fluorescent radiation intensity of analyte in specimen to fluorescent radiation intensity of pure element or compound, e.g., oxide is used in calculation in both fundamental parameter methods and in theoretical influence coefficient algorithms. Accuracy of calculated R_i is determined by uncertainties of atomic parameters, spectrometer geometry and also by X-ray tube spectral distribution. This paper presents the differences between R_i calculated using experimental and theoretical X-ray tube spectra evaluated by three different algorithms proposed by Pella et al., Ebel, and Finkelshtein–Pavlova. The calculations are performed for the most common targets, i.e., Cr, Mo, Rh and W. In this study, R_i is calculated for V, Cr, Mn, Fe, Co, Ni, Cu and Mo in steels as an example. The differences between R_i calculated using different X-ray tube spectrum algorithms are presented when pure element standard, multielement standard similar to the analyzed material and one pure element standard for all analytes is used in X-ray fluorescence analysis. The differences between R_i for intermediate-thickness samples (and also for thin films) and for X-ray tube, which ran for many hours, are also evaluated.     

Synthesis and evaluation of α-helix mimetics based on a trans-fused polycyclic ether: sequence-selective binding to aspartate pairs in α-helical peptides

Inspired by the topological similarity between ladder-like cyclic ether skeletons and α-helical peptides, a trans-fused 6/6/6/6 tetracyclic ether containing two hydroxyl groups separated by a distance of 4.8 Å was designed as a scaffold for a nonpeptidic α-helix mimetic. Two alkyl guanidinium groups were attached to the hydroxyl groups to develop a synthetic receptor for the specific recognition of i + 4 spaced aspartate pairs on the surface of an α-helical peptide. A circular dichroism (CD) titration showed that this mode of molecular recognition stabilizes α-helical structures of peptides containing i + 4 spaced aspartate pairs.     

Monte Carlo simulation of adsorption of binary and quaternary alkane isomers mixtures in zeolites: Effect of pore size and structure

Grand canonical Monte Carlo and configurational bias Monte Carlo techniques were employed to simulate the adsorption of binary mixtures of butane isomers and quaternary mixtures in nine zeolites at 300 K. For binary mixtures the results show there is a critical pore size, which is 10-membered-ring about 5.6 Å. The channel sizes of BEA, ISV, MOR and CFI are larger than this critical pore size, they prefer i-butane than n-butane, whereas TON with smaller channel size than critical pore size prefers n-butane than i-butane, but its selectivity decreases with pressure increasing. MFI, MEL and TER prefer i-butane than n-butane at low pressure, but with pressure increasing, the selectivity is reversed. BOG prefers i-butane than n-butane but the selectivity decreased with pressure increasing. It demonstrates that the adsorption and selectivity are controlled by both pore size and pore structure. The n-butane–i-butane–n-pentane–2-methylbutane quaternary mixtures adsorbed in these nine zeolites were studied, and the results show alkane chain length dependence at low pressure, but the adsorption is controlled by pore size and structure with pressure increasing in all the zeolites except for TON and BOG.     

One-pot synthesis of disulfide-linked N-sulfonylazetidin-2-imines via a copper-catalyzed multicomponent cascade reaction

A copper-catalyzed, three-component reaction between a sulfonyl azide, an alkyne, and a 2-aminothiophenol derived Schiff base is reported. This novel one-pot procedure involves a click reaction, a formal [2+2] cycloaddition, and S–S coupling, therefore, providing a unique method for the synthesis of novel disulfide-linked N-sulfonylazetidin-2-imines under mild conditions.     

Complexes of N-thiophosphorylthiourea (EtO)2P(O)CH2C6H4-4-[NHC(S)NHP(S)(OiPr)2] with Zn(II), Cd(II), Co(II) and Cu(PPh3)(I)

Reaction of O,O’-diisopropylthiophosphoric acid isothiocyanate (iPrO)₂P(S)NCS with diethyl 4-aminobenzylphosphonate (EtO)₂P(O)CH₂C₆H₄-4-NH₂ leads to the new N-thiophosphorylated thiourea (EtO)₂P(O)CH₂C₆H₄-4-[NHC(S)NHP(S)(OiPr)₂] (HL). Reaction of the potassium salt of HL with Zn(II), Cd(II) and Co(II) in aqueous EtOH leads to complexes of formula M(L-S,S’)₂ (ML₂). Heteroligand copper(I) complex of HL and triphenylphosphine was prepared by the reaction of the potassium salt KL and Cu(PPh₃)₃I. Copper in complex Cu(PPh₃)L is bound by one PPh₃ and one SCNPS fragment of the chelating ligand. Compounds obtained were investigated by IR, UV–Vis, ¹H and ³¹P{¹H} NMR spectroscopy, and microanalysis. The structures of HL and Cu(PPh₃)L were investigated by single crystal X-ray diffraction analysis.     

Intramolecularly lactam stapled oxyntomodulin analogues inhibit cancer cell proliferation in vitro

As a glucagon (GCG) receptor (GCGR) and glucagon-like peptide 1 (GLP-1) receptor (GLP-1R) dual agonist, oxyntomodulin (OXM) has been attracting scientific attentions due to its efficacies of suppressing appetite, increasing energy expenditure, and inducing body weight loss in obese humans. Based on the scaffold of native OXM, specific helix-favoring amino acids substitutions and the consequent salt bridge formations were believed to offer enhanced and balanced GCGR/GLP-1R activations through increasing α-helical conformation. Novel OXM analogues are obtained by intramolecular lactam stapling of positions [Glu16 & Lys20] or [Lys17 & Glu21] to further strengthen conformationally constrained stabilization. Even though the lactam staple does not provide additional dual GCGR/GLP-1R activations in vitro, the stapled OXM analogues are firstly reported to have higher or lower anti-PANC-1 cell proliferation activity, meanwhile which has no obvious inhibitory effect on the proliferation of HeLa cells. Therefore, it is speculated that the stapled analogues may have the potential to inhibit the proliferation of specific cancer cell types. Among the stapled peptides as well as their precursors, analogue 6 has the most prominent anti-PANC-1 proliferation activity with the IC₅₀ value of 115.1 μmol/L. Its mechanism of actions including effective signal pathways should be worth further investigations in future.     

A visual approach to stationary phase selectivity classification based on the Snyder–Dolan Hydrophobic-Subtraction Model

A novel type of stationary phase selectivity classification “triangle” has been developed based on the Snyder–Dolan (S–D) Hydrophobic-Subtraction Model, wherein the apices of a set of four triangles represent the relative contributions of steric hindrance (χ_S), hydrogen-bonding acidity (χ_A), hydrogen-bonding basicity (χ_B), cation-exchange capacity (χ_C) to selectivity. We found that “effective selectivity” of a stationary phase is mathematically given by the ratio of system dependent interaction coefficients but not their absolute values. Thus by normalizing the S*, A, B and C terms of the S–D model by H, we were able to obtain four parameters which fully define the chromatographic selectivity of the stationary phases. By examining the parameters in groups of three, we can represent all the result in a set of four “selectivity triangles”. The distinctive feature of this approach compared to the S–D phase classification scheme is that it allows the visualization of column selectivity by plotting three-dimensional data in a two-dimensional space. Moreover, it very clearly shows that the RPLC columns thus far characterized cover only a small fraction of separation selectivity space leaving a great deal of room for researchers to develop novel RPC materials. Various applications of these “selectivity triangles” will be discussed in this paper.     

Effect of size of metal ion on MS4N2 chromophore: Synthesis,spectral and single crystal X-ray structural studies on (2,2′-bipyridine)bis(N-cyclohexyl-N-methyldithiocarbamato)M(II) (M = zinc,cadmium)

Isomorphous complexes [Zn(S₂CN(Me)Cy)₂(bipy)] (1) and [Cd(S₂CN(Me)Cy)₂(bipy)] (2) (where Cy(Me)NCS₂⁻ = N-cyclohexyl-N-methyldithiocarbamate anion and bipy = 2,2′-bipyridine) have been synthesised. Their structures and spectroscopic properties have been studied by IR, ¹H and ¹³C NMR spectroscopy and single crystal X-ray analysis. IR spectrum of the complexes show the contribution of thioureide form to the structures. ¹H NMR spectra of the complexes showed the desheilding of methyl protons and H-1 of cyclohexyl group on complexation. The downfield shift of N¹³CS₂, methyl carbon and C-1 of cyclohexyl group carbon signals for 2 (205.5, 36.7 and 64.4 ppm) from the chemical shift value of 1 (204.2, 35.6 and 63.1 ppm) is attributed to the movement of more electron density from dithiocarbamate towards cadmium. Single crystal X-ray structures of 1 and 2 indicate that the central metal atom is in a distorted octahedral environment for both complexes. The presence of added 2,2′-bipyridine ligand in the coordination sphere of M(S₂CN(Me)Cy)₂ increases Zn–S distances and decreases S–Zn–S angles in 1 and slightly increases Cd–S distances in 2. S–Cd–S angles are not affected. This is due to the relatively larger size of the cadmium ion compared to zinc ion which alleviates the strain involved in transformation from tetrahedral to octahedral.     

Capillosananes S–Z,new sesquiterpenoids from the soft coral Sinularia capillosa

Chemical examination of the soft coral Sinularia capillosa resulted in the isolation of eight new sesquiterpenoids named capillosananes S–Z (1–8) and six known sesquiterpenes. The structures of the new compounds were determined on the basis of extensive spectroscopic analysis, including CD effects and Mosher method for the assignment of their absolute configurations. Capillosananes S–U (1–3) presented as the novel carbon skeletons with bicyclo[3,6,0] and bicyclo[4,5,0] systems, while capillosanane V (4) was characteristic of an unprecedented tricyclic skeleton. Capillosananes W–X (5–6) were assigned to the unusual dumortane-type sesquiterpenes. In addition, the absolute configurations of the stereoisomers of isodaucene-9,14-diol were assigned for the first time.     

Estimation of the 2.05 helix type i→i hydrogen bond energy at Aib-Oxa motif: an isodesmic approach

Bending at the valence angle N–C^α–C′ (τ) is a known control feature for attenuating the stability of the rare intramolecular i→i hydrogen bonded pseudo five-membered ring C₅ structures, the so called 2.0₅ helices, at Aib. The competitive 3₁₀-helical structures still predominate over the C₅ structures at Aib for most values of τ. However at Aib^∗, a mimic of Aib where the carbonyl O of Aib is replaced with an imidate N (in 5,6-dihydro-4H-1,3-oxazine = Oxa), in the peptidomimic Piv-Pro-Aib^∗-Oxa (1), the C₅i structure is persistent in both crystals and in solution. Here we show that the i→i hydrogen bond energy is a more determinant control for the relative stability of the C₅ structure and estimate its value to be 18.5 ± 0.7 kJ/mol at Aib^∗ in 1, through the computational isodesmic reaction approach, using two independent sets of theoretical isodesmic reactions.     

Ionic liquid-supported chiral saldach with tunable hydrogen bonding: synthesis,metalation with Fe(III) and in vitro antimicrobial susceptibility

New water-soluble methylimidazolium ionic liquids (MIILs) bearing N,N′-bis-(salicylidene)-R,R-1,2-diaminocyclohexane (saldach) scaffold, H₂(R¹)₂saldach(2-MeIm⁺X⁻)₂ (4a: R¹=H, X=Cl^–; 4b: R¹=H, X=PF₆^–; 4c: R¹=H, X=BF₄^–; 4d: R¹=ⁱPr, X=Cl^–; 4e: R¹=ⁱPr, X=PF₆^–; 4f: R¹=ⁱPr, X=BF₄^–), and their Fe(III) complexes have been synthesized and structurally characterized as well as their profile of antimicrobial susceptibility was identified. The new saldach-supported MIILs demonstrated a distinctly enhanced biocidal effect toward methicillin resistant Staphylococcus aureus (MRSA) and multidrug-resistant Escherichia coli (MDREC). Compound 4d is the most potent antibacterial agent and could inhibit the growth of all micro-organisms, except A. flavus, more effectively than standard antibiotics.     

Polarographic analysis of corticosteroids: Part 6. Mechanism of polarographic electroreduction of some Δ4-3-ketosteroids and Δ1,4-3-ketosteroids

Prednisolone and dexamethasone give waves in d.c. and normal pulse polarography and peaks in differential pulse polarography which correspond to a one-electron uptake. The transfer of the first electron is reversible and at pH < 7 (i₁) is preceded or at pH >7 (i₃) is followed by a proton transfer. Protonation occurs on the carbonyl group and pinacol is formed. At pH >7, wave i₃ is followed by wave i₄ which involves transfer of another proton and electron on the carbonyl group and yields the unsaturated alcohol. At pH <3, the radical formed in the first electron uptake is further protonated and is reduced in wave (i₁₊₂). In tetramethylammonium hydroxide solution, reduction of the side chains on C-17 occurs at more negative potentials. Reduction of testosterone and hydrocortisone follows a similar mechanism (A)—(G), but the second electron uptake in wave i₄ at pH >7 is not observed.