The configurations in solution of the biliverdin TXγ phorcabilin and isophorcabilin dimethyl esters

The configurations in solution of the title compounds have been attributed by ¹H NMR. Correlations with the absorption spectra show the importance of conformational restraints in the spectroscopic properties of the bilatriene system which is usually chosen as chromophore model for the phytochrome phototransformation.     

Stereoselective Organocatalyzed Synthesis of α‐Fluorinated β‐Amino Thioesters and Their Application in Peptide Synthesis

α‐Fluorinated β‐amino thioesters were obtained in high yields and stereoselectivities by organocatalyzed addition reactions of α‐fluorinated monothiomalonates (F‐MTMs) to N‐Cbz‐ and N‐Boc‐protected imines. The transformation requires catalyst loadings of only 1 mol % and proceeds under mild reaction conditions. The obtained addition products were readily used for coupling‐reagent‐free peptide synthesis in solution and on solid phase. The α‐fluoro‐β‐(carb)amido moiety showed distinct conformational preferences, as determined by crystal structure and NMR spectroscopic analysis.     

NMR spectroscopic conformational analysis of 4‐methylene‐cyclohexyl pivalate—The effect of sp2 hybridization

The conformational equilibrium of the axial/equatorial conformers of 4‐methylene‐cyclohexyl pivalate is studied by dynamic NMR spectroscopy in a methylene chloride/freon mixture. At 153 K, the ring interconversion gets slow on the nuclear magnetic resonance timescale, the conformational equilibrium (?ΔG°) can be examined, and the barrier to ring interconversion (ΔG^#) can be determined. The structural influence of sp² hybridization on both ΔG° and ΔG^# of the cyclohexyl moiety can be quantified.     

Ultrafast spectroscopy of a photoswitchable 30-amino acid de novo synthesized peptide

The ultrafast photoresponse of small, often cyclic peptides with azobenzene units has widely been investigated during the last years. Both the photoisomerization of the optical switch as well as the different conformational states of the peptide moiety can be characterized by optical spectroscopy. Here, we investigate the fast photoisomerization dynamics of an α-helical 30mer azobenzene peptide. The peptide is based on a construct used for the assembly of di-heme-binding maquettes. The femtosecond to picosecond photodynamics for the trans to cis isomerization of the optical switch was found to occur slower upon its insertion in the peptide construct. Both isomers are sufficiently photostable to allow spectroscopic analysis of conformational states, since the thermal cis–trans relaxation occurs over a period of several hours. This approach thus offers the possibility for the de novo design of photoresponsive chromopeptides which could be instrumental in unravelling fundamental dynamic features of assembly/disassembly triggered by fast photoswitches.     

Chiral discrimination in biliverdin (S)-amino acids,II: Structural variations of the amino acid functional groups

The Biliverdin-(S)-amino acid derivatives2–21 have been synthesized, and are subject to a thorough c. d. and u. v.-vis. electronic absorption analysis in the bilatriene chromophoric region. It is shown that the extent of chiral discrimination of the bilatriene helices is particularly sensitive towards structural variations of the amino acids bound to the propionic side chains. Thus, a pronounced decrease of chiral induction occurs if hydrogen bonding between one of the two essential coordination sites of the amino acid entity and the bilatriene backbone is disturbed. Accordingly, derivatives of (S)-amino acidt-butyl esters (3,5,7,16 and17) andN-substituted (S)-amino acids (8–10, 20 and21) generally display weak c. d. spectra. If additional polar groups are present in bis(amino acid) derivatives mutual interferences of the adjacent side chains must be taken into account. The attenuations of -values observed for the bis(serine) and bis(aspartic acid) compounds14 and15 thus are mainly due to intramolecular interchain interactions. The results provide evidence in support of the proposed mechanism of chiral discrimination in biliverdin amino acids.Dedicated to Prof. Dr.Kurt L. Komarek on the occasion of his 60th birthday.     

On the Use of a Supramolecular Coarse‐Grained Model for the Solvent in Simulations of the Folding Equilibrium of an Octa‐β‐peptide in MeOH and H2O

Molecular dynamics (MD) simulation can give a detailed picture of conformational equilibria of biomolecules, but it is only reliable if the force field used in the simulation is accurate, and the sampling of the conformational space accessible to the biomolecule shows many (un)folding transitions to allow for precise averages of observable quantities. Here, the use of coarse‐grained (CG) solvent MeOH and H₂O models to speed up the sampling of the conformational equilibria of an octa‐β‐peptide is investigated. This peptide is thought to predominantly adopt a 3₁₄‐helical fold when solvated in MeOH, and a hairpin fold when solvated in H₂O on the basis of the NMR data. Various factors such as the chirality of a residue, a force‐field modification for the solute, coarse‐graining of the solvent model, and an extension of the nonbonded interaction cut‐off radius are shown to influence the simulated conformational equilibria and the agreement with the experimental NMR data for the octa‐β‐peptide.     

A Multicomponent Conjugation Strategy to Unique N‐Steroidal Peptides: First Evidence of the Steroidal Nucleus as a β‐Turn Inducer in Acyclic Peptides

Constraining small peptides into specific secondary structures has been a major challenge in peptide ligand design. So far, the major solution for decreasing the conformational flexibility in small peptides has been cyclization. An alternative is the use of topological templates, which are able to induce and/or stabilize peptide secondary structures by means of covalent attachment to the peptide. Herein a multicomponent strategy and structural analysis of a new type of peptidosteroid architecture having the steroid as N‐substituent of an internal amide bond is reported. The approach comprises the one‐pot conjugation of two peptide chains (or amino acid derivatives) to aminosteroids by means of the Ugi reaction to give a unique family of N‐steroidal peptides. The conjugation efficiency of a variety of peptide sequences and steroidal amines, as well as their consecutive head‐to‐tail cyclization to produce chimeric cyclopeptide–steroid conjugates, that is, macrocyclic lipopeptides, was assessed. Determination of the three‐dimensional structure of an acyclic N‐steroidal peptide in solution proved that the bulky, rigid steroidal template is capable of both increasing significantly the conformational rigidity, even in a peptide sequence as short as five amino acid residues, and inducing a β‐turn secondary structure even in the all‐s‐trans isomer. This report provides the first evidence of the steroid skeleton as β‐turn inducer in linear peptide sequences.     

Conformational Preferences of a β‐Octapeptide as Function of Solvent and Force‐Field Parameters

The ability to design properly folded β‐peptides with specific biological activities requires detailed insight into the relationship between the amino acid sequence and the secondary and/or tertiary structure of the peptide. One of the most frequently used spectroscopic techniques for resolving the structure of a biomolecule is NMR spectroscopy. Because only signal intensities and frequencies are recorded in the experiment, a conformational interpretation of the recorded data is not straightforward, especially for flexible molecules. The occurrence of conformational and/or time averaging, and the limited amount and accuracy of experimental data hamper the precise conformational determination of a biomolecule. In addition, the relation between experimental observables with the underlying conformational ensemble is often only approximately known, thereby aggravating the difficulty of structure determination of biomolecules. The problematic aspects of structure refinement based on NMR nuclear Overhauser effect (NOE) intensities and ³J‐coupling data are illustrated by simulating a β‐octapeptide in explicit MeOH and H₂O as solvents using three different force fields. NMR Data indicated that this peptide would fold into a 3₁₄‐helix in MeOH and into a hairpin in H₂O. Our analysis focused on the conformational space visited by the peptide, on structural properties of the peptide, and on agreement of the MD trajectories with available NMR data. We conclude that 1) although the 3₁₄‐helical structure is present when the peptide is solvated in MeOH, it is not the only relevant conformation, and that 2) the NMR data set available for the peptide, when solvated in H₂O, does not provide sufficient information to derive a single secondary structure, but rather a multitude of folds that fulfill the NOE data set.     

Hemicarbasucrose: Turning off the Exoanomeric Effect Induces Less Flexibility

Hemicarbasucrose, a close congener of sucrose in which the endocyclic oxygen atom of the glucose moiety is replaced by a methylene group was synthesized for the first time. The conformational behaviour of hemicarbasucrose was studied by a combination of molecular mechanics and NMR spectroscopy (J and NOE data). It was shown that the carbadisaccharide populates two distinct conformational families in solution, the normal syn‐ψ conformation, which is the predominating conformation of the parent natural O‐glycoside, and the anti‐ψ conformation, which has not been detected for the O‐disaccharide. Interestingly, the hemicarbasucrose is less flexible than its natural congener.     

The influence of N-protected amino acid residues on the cis/trans isomerism of proline moieties in peptides

¹³C NMR spectroscopy is an excellent tool for studying the influence of N-protecting groups on the cis/trans isomerism of proline residues in proline peptides. This communication demonstrates the usefulness of ¹³C NMR spectroscopy in investigating conformational problems in protein and peptide chemistry.     

Mimicking Chitin: Chemical Synthesis,Conformational Analysis,and Molecular Recognition of the β(1→3) N‐Acetylchitopentaose Analogue

Mimicking Nature by using synthetic molecules that resemble natural products may open avenues to key knowledge that is difficult to access by using substances from natural sources. In this context, a novel N‐acetylchitooligosaccharide analogue, β‐1,3‐N‐acetamido‐gluco‐pentasaccharide, has been designed and synthesized by using aminoglucose as the starting material. A phthalic group has been employed as the protecting group of the amine moiety, whereas a thioalkyl was used as the leaving group on the reducing end. The conformational properties of this new molecule have been explored and compared to those of the its chito analogue, with the β‐1,3 linkages, by a combined NMR spectroscopic/molecular modeling approach. Furthermore, the study of its molecular recognition properties towards two proteins, a lectin (wheat germ agglutinin) and one enzyme (a chitinase) have also been performed by using NMR spectroscopy and docking protocols. There are subtle differences in the conformational behavior of the mimetic versus the natural chitooligosaccharide, whereas this mimetic is still recognized by these two proteins and can act as a moderate inhibitor of chitin hydrolysis.     

Escherichia coli β‐Galactosidase Inhibitors through Modifications at the Aglyconic Moiety: Experimental Evidence of Conformational Distortion in the Molecular Recognition Process

Herein, we describe the use of thioglycosides as glycosidase inhibitors by employing novel modifications at the reducing end of these glycomimetics. The inhibitors display a basic galactopyranosyl unit (1→4)‐bonded to a 3‐deoxy‐4‐thiopentopyranose moiety. The molecular basis of the observed inhibition has been studied by using a combination of NMR spectroscopy and molecular modeling techniques. It is demonstrated that these molecules are not recognized by Escherichia coli β‐galactosidase in their ground‐state conformation, with a conformational selection process taking place. In fact, the observed conformational distortion depends on the chemical nature of the compounds and results from the rotation around the glycosidic linkage (variation of Φ or Ψ) or from the deformation of the six‐membered ring of the pentopyranose. The bound conformations of the ligand are adapted in the enzymatic pocket with a variety of hydrogen‐bond, van der Waals, and stacking interactions.     

Beta-Ala containing peptides: potentials in design and construction of bioactive peptides and protein secondary structure mimics

In recent years, there has been increasing interest in de novo design and construction of novel synthetic peptides that mimic protein secondary structures, i.e., turns, helices and sheets. The unique structural influences exerted by unsubstituted, non-coded, non-chiral beta-amino acid, i.e., beta-alanine (beta-Ala; 3- or beta- aminopropionic acid) on peptide backbone, when inserted into peptide chain comprised alpha-amino acids, offer an excellent opportunity to design and construct diverse well-defined three-dimensional structures. Our current understanding of folding-unfolding behavior of the beta-Ala residues relies primarily from an examination of conformational preferences of a large number of short cyclic- as well as acyclic beta-Ala containing peptides investigated using single crystal X-ray diffraction analysis. In addition, theoretical conformational energy calculations and different spectroscopic techniques: 1H NMR, FT-IR and CD, have also been employed although, to a lesser extent. The obtainable results tend to reveal overwhelming preferences of the beta-Ala moiety for the folded gauche (mu approximately +/-65+/-10 degrees conformation in cyclic- and for an extended trans (mu approximately +/-165+/-10 degrees) as well as gauche (mu approximately +/-65+/-10 degrees) orientations in acyclic beta-Ala containing peptides. The results also indicate that in short linear beta-Ala containing peptides, the specific influence of selective neighboring side-chain substituents e.g. linear- or cyclic symmetrically C(alpha,alpha)-disubstituted glycines and other conformational constraints, may be significant in controlling the overall folded-unfolded topographical features across the two methylene units (-CbetaH2-CalphaH2-) of the beta-Ala residue. Taking into consideration the wide occurrence of beta-Ala moiety in animal and plant kingdoms and the remarkable structural versatility of the peptides incorporating beta-Ala residue(s), together with appreciable resistance towards enzymatic degradation, hold strong promise for biophysicists and biochemists not only to design molecules that fold to mimic protein secondary structures but also to develop potent peptide analogs and peptidomimetics displaying unique pharmaceutical properties.     

Structural Studies and Anticancer Activity of a Novel Class of β‐Peptides

Functionalized oligomeric organic compounds with well‐defined β‐proline scaffold have been synthesized by a cycloadditive oligomerization approach in racemic and enantiopure forms. The structure of the novel β‐peptides was investigated by NMR spectroscopic and X‐ray methods determining the conformational shapes of the β‐proline oligomers in solution and solid states. The main structural elements subject to conformational switches are β‐peptide bonds between 5‐arylpyrrolidine‐2‐carboxylic acid units existing in Z/E configurations. The whole library of short β‐peptides and intermediate acrylamides has been tested on antiproliferative activity towards the hormone‐refractory prostate cancer cell line PC‐3 revealing several oligomeric compounds with low micromolar and submicromolar activities. Bromine‐substituted dimeric and trimeric acrylamides induced caspase‐dependent apoptosis of PC‐3 cells through cell‐cycle arrest and mitochondrial damage.     

胸腺素α1类似物的定点PEG修饰及其免疫活性评价

PEG修饰是改善蛋白质及肽类药物药代动力学特性的有效途径。然而与蛋白质相比，肽类化合物的分子较小，PEG的分子体积较大，其长链很可能会遮蔽肽的活性位点。因此，肽类化合物PEG修饰的位置和数量对于保持肽的生物活性至关重要。为阐明PEG修饰的位置与肽生物活性之间的关系，对肽类药物日达仙（胸腺素α1，Tα1）进行了定点修饰。Tα1具有α-螺旋、β-转角和无规卷曲的结构区域。分别在这些区域选择不同的位点进行PEG修饰。PEG的定点修饰是通过引入Cys，利用其-SH与mPEG-MAL的特异性反应而实现的。Con A刺激下的脾细胞产生IFN-γ试验的初步结果表明，PEG修饰对活性的影响与修饰的位置有一定的关系，大多数情况下，PEG修饰能保持Tα1的免疫活性。PEG修饰的位点对于保持肽的生物活性是很重要的。     

The effect of the t-butyl substituent on polymer properties in homopolymer systems

The effect of a bulky substituent on properties of different homopolymers has been examined. The substituent is the t-butyl moiety attached to a benzene ring found in the repeat units of the homopolymers of polyesters, polyarylates, polyamides, and polyaramides. These polymers have been prepared by melt, solution, or interfacial techniques. The source of the t-butyl group is mainly from 5-t-butylisophthalic acid (5TBIA) and comparisons are generally made with corresponding homopolymers based on isophthalic acid. The effect of the t-butyl group is shown by comparison of the properties of these homopolymers. Thermal and mechanical (tensile and impact) properties, density, water absorption, solubility, and processability are discussed. Differences in these properties are attributed to the t-butyl group and are based on intermolecular and intramolecular interactions that include increased free volume, chain stiffening, and conformational changes.     

Effect of the Medium on the Equilibrium between Stereoisomeric Six- and Seven-Membered Cyclic chair-Like Acetals. Role of Nonspecific and Specific Interactions

Principles for establishing the nature of solvation effects in stereoisomeric equilibria have been formulated. Using ¹H NMR spectroscopy, the equilibrium constants have been determined in 12 solvents for the endo and exo isomers of 1,9,10,11,12,12-hexachloro-4,6-dioxatricyclo[7.2.1.02,8]dodec-10-ene which is characterized by a high barrier to stereoisomeric transformations. The results of correlation analysis have shown that solvation of the conformers with dissimilar orientations of the hexachloronorbornene fragment with respect to the chair-like acetal moiety is determined by the polarity and proton-acceptor properties of the medium. Comparison with the data on solvent effect on the equilibrium between 2-isopropyl-5-methoxy-1,3-dioxane epimers suggests that the formation of H-complexes is controlled by electronic and conformational factors.     

Structure determination of a tetradecapeptide mimicking the RXVRG consensus sequence recognized by a Xenopus laevis skin endoprotease: An approach based on simulated annealing and 1H NMR

Summary The tetradecapeptide of sequence H-Asp-Val-Asp-Glu-Arg ⁵-Asp-Val-Arg-Gly⁹-Phe-Ala-Ser-Phe-Leu-NH₂ is recognized by a putative maturation endoprotease of the Xenopus laevis skin, which cleaves between Arg⁸ and Gly⁹. A conformational search has been performed on this peptide by simulated annealing calculations. Two different models in agreement with the NMR data were found. The conformational difference between the two types of model is located in the consensus sequence, i.e., from Arg⁵ to Gly⁹.     

Synthese des Flechtenmakrolids (+)-Aspicilin mit Photolactonisierung als Schlüsselreaktion

Synthesis of the Lichen Macrolide (+)-Aspicilin Using Photolactonization as a Key Reaction (+)-Aspicilin, obtained from a lichen source of the Black Forest, has been proven to have the absolute configuration depicted by formula la . It is easily built up from phenol ( 14a ), 1,9-nonanediol ( 13a ), and (?)-(S-) methyloxiarane ( 6 ) (cf. Scheme 2). The latter building block provides the first stereogenic center C(17). The heterocycle is produced by photolactonization, fairly early during the course of the synthesis. The second stereogenic center is generated diastereoselectively at C(6) in compound 8 , conveniently available from photolactone 9a or 9b / 9c . Its absolute configuration depends on the kind of reducing agent and is controlled by long-range conformational transmission of chiral information. To explore the cause of stereoselection, 2D-NMR spectroscopy, X-ray structural analysis, and/or computer-aided conformational search followed by energy minimization have been used extensively, revealing the importance of the local conformation of the lactone moiety. Compound 8 , on treatment with Yamamoto's reagent, affords pre-target compound 7a almost exclusively. The latter compound, on pyridine-accelerated dihydroxylation with OsO₄, gives preferentially (+)-Aspicilin.     

Tuning Aqueous Supramolecular Polymerization by an Acid-Responsive Conformational Switch

Besides their widespread use in coordination chemistry, 2,2’-bipyridines are known for their ability to undergo cis–trans conformational changes in response to metal ions and acids, which has been primarily investigated at the molecular level. However, the exploitation of such conformational switching in self-assembly has remained unexplored. In this work, the use of 2,2’-bipyridines as acid-responsive conformational switches to tune supramolecular polymerization processes has been demonstrated. To achieve this goal, we have designed a bipyridine-based linear bolaamphiphile, 1 , that forms ordered supramolecular polymers in aqueous media through cooperative aromatic and hydrophobic interactions. Interestingly, addition of acid (TFA) induces the monoprotonation of the 2,2’-bipyridine moiety, leading to a switch in the molecular conformation from a linear (trans) to a V-shaped (cis) state. This increase in molecular distortion along with electrostatic repulsions of the positively charged bipyridine-H⁺ units attenuate the aggregation tendency and induce a transformation from long fibers to shorter thinner fibers. Our findings may contribute to opening up new directions in molecular switches and stimuli-responsive supramolecular materials.