Backbone modification of β-hairpin-forming tetrapeptides in asymmetric acyl transfer reactions

Synthetic oligopeptides as mimics of enzymes have been increasingly exploited as catalysts for asymmetric reactions, but highly effective oligopeptide catalysts with relatively low molecular weight are still in great demand. In this paper, we showed the conformational engineering of the β-hairpin-forming tetrapeptide 4 which was first reported by Miller's group as the catalyst for the asymmetric acyl transfer reaction of trans-2-(N-acetylamino)cyclohexan-1-ol (k(rel)=28). Through our backbone modification strategy, thioamide and sulfonamide as the isosteres of amide were introduced in the β-hairpin secondary structure. The thioxo peptides also adopt β-hairpin conformations as the oxopeptide supported by the combined use of NMR, IR, and X-ray techniques. Thioxo tetrapeptide 14 formed a more constrained β-hairpin conformation and therefore delivered much higher enantioselectivity (k(rel)=109) in the same reaction. Moreover, the examination of the conformational changes of tetrapeptide 8 upon the protonation of the N(π)-methylhistidine moiety provided evidence to explain the variation of its catalytic efficiency in the asymmetric acyl-transfer reaction.     

Turn-directed folding dynamics of β-hairpin-forming de novo decapeptide Chignolin

Realistic mechanistic pictures of β-hairpin formation, offering valuable insights into some of the key early events in protein folding, are accessible through short designed polypeptides as they allow atomic-level scrutiny through simulations. Here, we present a detailed picture of the dynamics and mechanism of β-hairpin formation of Chignolin, a de novo decapeptide, using extensive, unbiased molecular dynamics simulations. The results provide clear evidence for turn-directed broken-zipper folding and reveal details of turn nucleation and cooperative progression of turn growth, hydrogen-bond formations, and eventual packing of the hydrophobic core. Further, we show that, rather than driving folding through hydrophobic collapse, cross-strand side-chain packing could in fact be rate-limiting as packing frustrations can delay formation of the native hydrophobic core prior to or during folding and even cause relatively long-living misfolded or partially folded states that may nucleate aggregative events in more complex situations. The results support the increasing evidence for turn-centric folding mechanisms for β-hairpin formation suggested recently for GB1 and Peptide 1 based on experiments and simulations but also point to the need for similar examinations of polypeptides with larger numbers of cross-strand hydrophobic residues.     

Synthesis and structural investigations of functionalizable hybrid β-hairpin

The solution and solid state conformations of a designed β-hairpin containing functionalizable α,β-unsaturated γ-amino acids at the antiparallel β-strands and a single step transformation to its saturated γ-peptide analogue are studied.     

Theoretical insights into the catalytic mechanism of β-hexosaminidase

The enzyme (β-Hex) has a specific role in the degradation of a particular type of glycolipid, the GM2 ganglioside. This specificity is also manifested by its unusual mechanism of substrate-assisted catalysis, which is considered to be an alternative pathway for the breakage of glycosidic bonds. We have studied its catalytic mechanism using a small model of the enzyme: substrate Michaelis complex with DFT and MP2/MP3 methods. The results reflect the intrinsic chemical reactivity of the active site, decoupled from the long-range enzyme electrostatic field. The mechanism supports, and adds further atomic detail, on the earlier mechanistic suggestions based on experimental data. Moreover, we also have compared the geometry and full potential energy surface obtained with nine different exchange–correlation functionals. It was surprising that the B3LYP activation energies were lower than the ones from some of the hybrid meta functionals (known by their excellent performance on kinetics) by as much as 10 kcal/mol and lower than the MP2 energies by more than 12 kcal/mol. It is known that B3LYP underestimates barriers but underestimations of this extent are unusual and surprising. The effect of the theoretical method on the geometry, usually supposed to be less significant, had in some cases a relevant influence in the mechanism. Therefore, a more thoughtful choice should be made when choosing a methodology for geometry optimization.     

Self-assembly of chiral trans-cyclobutane-containing β-dipeptides into ordered aggregates

Two chiral synthetic β-dipeptides have been constructed, one with two trans-cyclobutane residues and the other with one trans and one cis fragment, 1 and 2, respectively, and investigated to get insight into the non-covalent interactions responsible for their self-assembly to form ordered aggregates, as well into parameters such as their morphology and size. Experimental evidence of the formation of these assemblies was provided by spectroscopy, microscopy and X-ray diffraction experiments that suggest the formation of nanoscale helical aggregates. This process involves a conformational change in the molecules of each dipeptide with respect to the preferred conformation of the isolated molecules in solution. A high-resolution NMR spectroscopy study allowed the determination of the dynamics of the gelation process in [D(8)]toluene and the sol-gel transition temperature, which was around 270 K in this solvent at a concentration of 15 mM. NMR spectroscopy experiments also provided some information about conformational changes involved in the sol-gel transition and also suggested a different gel packing for each dipeptide. These observations have been nicely explained by computational studies. The self-assembly of the molecules has been modelled and suggested a head-to-head molecular arrangement for 1 and a head-to-tail arrangement for 2 to give helical structures corresponding to hydrogen-bonded single chains. These chains interact with one another in an antiparallel way to afford bundles, the significant geometry parameters of which fit well to the main peaks observed in wide-angle X-ray diffraction spectra of the aggregates in the solid state.     

Synthesis and conformational studies of a hybrid β-alanine-morpholine tetramer

A new morpholine-containing foldameric hybrid peptide was synthesized in solution phase, and the conformational preferences were assessed by means of NMR and molecular modeling calculations. All data suggested the existence of two equilibrating conformations involving hydrogen-bonds in the major rotamer. Moreover, calculations on higher model foldamers indicated seven-membered ring hydrogen-bond forming γ-turns as the main driving force in the stabilization of helix-folded conformations. Thus, this study suggests the possibility of using morpholine-3-COOH as a proline surrogate to generate higher α/β hybrid peptides.     

Distorted aryl homochirality controlled by β-sheet folding

Distortion of planar aromatics occurs in the fused rings conjugated with bulky substituents, which generates racemic enantiomers with high transformation energy barriers. However, direct synthesis of homochiral distorted aryl compounds is a very challenging task. Here, we presented a molecular folding strategy to control distorted aryl homochirality. Amino acids and their derivatives conjugated on the polycyclic aromatic hydrocarbons including benzenes, naphthalenes and triphenylenes, which formed parallel β-sheet arrays through intramolecular hydrogen bonds. The folding behavior enabled distorted or twisted geometry of aromatics, of which the handedness was associated with the absolute chirality of amino acids. X-ray crystallography, theoretical calculations and circular dichroism spectroscopy verified the distorted homochirality in the solid and solution phase. The relatively small rotational barrier between the enantiomers made the molecule sensitive to the environment and thus realized the solvent-controlled chiral inversion. The β-sheet folding strategy can be widely used in polycyclic aromatic hydrocarbons with various functions, which provided a promising strategy to control inherent chirality of aromatics with adaptive chiroptical responses.     

Cycloaddition of cyclohexa-2,4-dienones with β-nitroacrylates: a short and efficient entry into bicyclo[2.2.2]octanes endowed with β-nitro-ester and β-amino ester functionality

Regio- and stereoselective cycloaddition of β-nitroacrylates with electron deficient cyclohexa-2,4-dienones leading to highly functionalised bicyclo[2.2.2]octanes having the β-nitroester group and their transformation to bicyclo[2.2.2]octanes having β-aminoester functionality is described.     

One-pot conversion of carbamates of unsaturated β-aminoesters into unsaturated β-lactams by use of trimethylsilyl iodide

Trimethylsilyl iodide (TMSI) is introduced as an efficient reagent for the one-pot and direct transformation of carbamates of unsaturated β-aminoesters into the corresponding α-methylene-β-lactams and α-arylidene-β-lactams. The mild reaction conditions, excellent yields and easy work-up procedures make it a useful alternative to previously applied procedures for the rapid synthesis of β-lactams from easily available Baylis-Hillman adducts.     

Crowding alters the folding kinetics of a β-hairpin by modulating the stability of intermediates

Crowded environments inside cells exert significant effects on protein structure, stability, and function, but their effects on (pre)folding dynamics and kinetics, especially at molecular levels, remain ill-understood. Here, we examine the latter for, as an initial candidate, a small de novo β-hairpin using extensive all-atom molecular dynamics simulations for crowder volume fractions φ up to 40%. We find that crowding does not introduce new folding intermediates or misfolded structures, although, as expected, it promotes compact structures and reduces the accessible conformational space. Furthermore, while hydrophobic-collapse-mediated folding is slightly enhanced, the turn-directed zipper mechanism (dominant in crowder-free situations) increases many-fold, becoming even more dominant. Interestingly, φ influences the stability of the folding intermediates (FI(1) and FI(2)) in an apparently counterintuitive manner, which can be understood only by considering specific intrachain interactions and intermediate (and hierarchical) structural transitions. For φ values <20%, native-turn formation is enhanced, and FI(1), characterized by a hairpin structure but slightly mismatched hydrophobic contacts, increases in frequency, thus enhancing eventual folding. However, higher φ values impede native-turn formation, and FI(2), which lacks native turns, re-emerges and increasingly acts as a kinetic trap. The change in the stability of these intermediates with φ strongly correlates with the hierarchical folding stages and their kinetics. The results show that crowding assists intermediate structural changes more by impeding backward transitions than by promoting forward transitions and that a delicate competition between reduction in configuration space and introduction of kinetic traps along the folding route is key to understanding folding kinetics under crowded conditions.     

Computational study on the encapsulation of ethylparaben into β-cyclodextrin

Two models namely A and B were considered to investigate the inclusion process of ethylparaben into β-CD cavity by means PM3, HF/6-31G (d) and B3LYP/6-31G (d). The obtained results with PM3 method clearly indicate that the formed complexes are energetically favored with or without solvent; the B complex is found more favored than A complex. The calculated deformations energies show that the geometry of β-CD is deformed in the complexation process on the other hand the ethylparaben do not undergo deformation. Finally, From NBO analysis, the donor and acceptor interactions between ethylparaben and β-CD were analyzed and discussed.     

Conversion of Nitroalkenes into β-(Trichloromethyl) Nitroalkanes

The cesium fluoride-catalyzed reaction of (trichloromethyl) - trimethylsilane with conjugated nitroalkenes affords β-(trichloromethyl)nitroalkanes.     

Unexpected Grob-type fragmentation of vinylogous β-silyloxy-cyclobutanone into γ-lactone

An unusual formal oxy transposition of vinylogous β-silyloxy-cyclobutanone 1(a 1,5-difunctionalized substrate) under mild acidic conditions(aqueous HF in CH_3CN at 0℃) to the decalinic y-lactone 2 was described.A plausible mechanistic pathway involving the Grob-type fragmentation and intramolecularγ-Iactonization was proposed.     

Synthesis of β-pyrrolic-modified porphyrins and their incorporation into DNA

A synthetic methodology for the synthesis of various β-pyrrolic-functionalised porphyrins and their covalent attachment to 2'-deoxyuridine and DNA is described. Palladium(0)-catalysed Sonogashira and copper(I)-catalysed Huisgen 1,3-dipolar cycloaddition reactions were used to insert porphyrins into the structure of 2'-deoxyuridine and DNA. Insertion of a porphyrin into the middle of single-stranded CT oligonucleotides possessing a 5'-terminal run of four cytosines was shown to trigger the formation of pH- and temperature-dependent i-motif structures. Porphyrin insertion also led to the aggregation of single-stranded purine-pyrimidine sequences, which could be dissociated by heating at 90 °C for 5 min. Parallel triplexes and anti-parallel duplexes were formed in the presence of the appropriate complementary strand(s). Depending on the modification, porphyrins were placed in the major and minor grooves of duplexes and were used as bulged intercalating insertions in duplexes and triplexes. In general, the thermal stabilisation of parallel triplexes possessing porphyrin-modified triplex-forming oligonucleotide (TFO) strands was observed, whereas anti-parallel duplexes were destabilised. These results are compared and discussed on the basis of the results of molecular modelling calculations.     

Using one-step perturbation to predict the folding equilibrium of differently stereochemically substituted β-peptides

The one-step perturbation technique is used to predict the folding equilibria for 16 peptides with different stereochemical side-chain substitutions through one or two long-time simulations, one of an unphysical reference state and another of one of the 16 peptides for which many folding events can be sampled. The accuracy of the one-step perturbation results was investigated by comparing to results available from long-time MD simulations of particular peptides. Their folding free energies were reproduced within statistical accuracy. The one-step perturbation results show that an axial substitution at either the C(α) or the C(β) position destabilizes the 3(14)-helical conformation of the hepta-β-peptide, which is consistent with data inferred from experimental CD spectra. The methodology reduces the number of required separate simulations by an order of magnitude.     

Anticancer β-hairpin peptides: membrane-induced folding triggers activity

Several cationic antimicrobial peptides (AMPs) have recently been shown to display anticancer activity via a mechanism that usually entails the disruption of cancer cell membranes. In this work, we designed an 18-residue anticancer peptide, SVS-1, whose mechanism of action is designed to take advantage of the aberrant lipid composition presented on the outer leaflet of cancer cell membranes, which makes the surface of these cells electronegative relative to the surface of noncancerous cells. SVS-1 is designed to remain unfolded and inactive in aqueous solution but to preferentially fold at the surface of cancer cells, adopting an amphiphilic β-hairpin structure capable of membrane disruption. Membrane-induced folding is driven by electrostatic interaction between the peptide and the negatively charged membrane surface of cancer cells. SVS-1 is active against a variety of cancer cell lines such as A549 (lung carcinoma), KB (epidermal carcinoma), MCF-7 (breast carcinoma), and MDA-MB-436 (breast carcinoma). However, the cytotoxicity toward noncancerous cells having typical membrane compositions, such as HUVEC and erythrocytes, is low. CD spectroscopy, appropriately designed peptide controls, cell-based studies, liposome leakage assays, and electron microscopy support the intended mechanism of action, which leads to preferential killing of cancerous cells.     

One-pot easy conversion of Baylis-Hillman adducts into carbamates of unsaturated β-amino acids

An easy, one-pot transformation of Baylis-Hillman adducts into carbamates of unsaturated β-amino acids, for example, 2-(aryl(methoxycarbonylamino)methyl)acrylic acid methyl esters 7 and 2-(methoxycarbonyl aminomethyl)-3-arylacrylic acid methyl esters 8 via reaction with the Burgess reagent is described.     

Coassembly of enantiomeric amphipathic peptides into amyloid-inspired rippled β-sheet fibrils

Amphipathic peptides composed of alternating hydrophobic and hydrophilic amino acids self-assemble into amyloid-inspired, β-sheet nanoribbon fibrils. Herein, we report a new fibril type that is formed from equimolar mixtures of enantiomeric amphipathic peptides (L- and D-(FKFE)(2)). Spectroscopic analysis indicates that these peptides do not self-sort and assemble into enantiomeric fibrils composed of all-l and all-d peptides, but rather coassemble into fibrils that contain alternating L- and D-peptides in a "rippled β-sheet" orientation. Isothermal titration calorimetry indicates an enthalpic advantage for rippled β-sheet coassembly compared to self-sorted β-sheet assembly of enantiomeric peptides.     

Semipinacol rearrangement of cis-fused β-lactam diols into keto-bridged bicyclic lactams

The 6-azabicyclo[3.2.1]octane ring system, prevalent in a range of biologically active molecules, is prepared through a novel semipinacol rearrangement utilizing a cyclic phosphorane or sulfite intermediate. The rearrangement proceeds with exclusive N-acyl group migration of a β-lactam ring and results in carbonyl functionality at the 7- and bridging 8-position of the bicycle. Precursor ring-fused β-lactam diols are prepared through a sequence of 4-exo trig carbamoyl radical cyclization, regioselective dithiocarbamate group elimination, and dihydroxylation.