某些环肽及其相应线型肽在不同溶剂中构象的CD谱研究

We used CD spectroscopy to study the conformations of three cyclic peptides (CP10E: cyclo[Glu(OBz1)-Pro-Gly-Glu(OBzl)-Gly]2, CP10K: cyclo[Lys(Z)-Pro-Gly-Lys(Z)-Gly]2, CP12K: cyclo[Phe-Lys(Z)-Pro-Gly-Lys(Z)-Gly]2 and their correspondent linear peptides (LP10E: Boc-[Glu(OBzl)-Pro-Gly-Glu(OBzl)-Gly]2-OPac, LP10K: Boc-[Lys(Z)-Pro-Lys(Z)-Pro]2-OMe, LP 12K: Bao- [-Lys(Z)-Pro-Gly-Lys(Z)-Gly]2- OMe) in three solvents of different polarity (chloroform, acetonitrile, 2,2,2-triliuroethanol), and it was found that all of linear and cyclicpeptides exists asγ-turn conformation in chloroform, however, in TFE＆ CH3CN solutions, the three linear peptides are inβ Ⅱ-turn conformations. CP10E isβI-turn conformation, CP10K ＆CP12K exists in more than one types of turn conformations. On the basis of our experiments, it was concluded: 1) In the presence of conformational constrained amino acids short linear peptides form obvious secondary structure; 2)The solvent polarity has influence on the peptide conformation and this influence on linear peptides is greater than that on cyclic peptides; 3)The backbone of cyclic peptide has constraint effect on its conformation and makes the secondary structure of cyclic peptide different from that of its relative linear peptide. This information might give some cules in the design of bioactive peptides with different receptor selectivity.     

Initial conformations of macrocyclic compounds with rotational symmetry generated from a molecular fragment

An algorithm is described for generating atomic Cartesian coordinates of conformations of macrocyclic molecules possessing exact rotational or rotation-reflection symmetries. A fragment representing the asymmetric unit of the molecule is suitably oriented in space, and then a symmetry operator is applied to generate the initial coordinates of the molecule. An empirical force field of interatomic interactions is used to generate equilibrium conformations. Results of calculations performed on two cyclic polylactones and one crown ether using this approach are given. They reveal that symmetric conformations of these molecules are often preferred. Since the latter conformations are probably responsible for the specialized properties of these molecules, this method should facilitate doing theoretical studies on these kinds of compounds.     

Structure prediction of cyclic peptides by molecular dynamics + machine learning

Recent computational methods have made strides in discovering well-structured cyclic peptides that preferentially populate a single conformation. However, many successful cyclic-peptide therapeutics adopt multiple conformations in solution. In fact, the chameleonic properties of some cyclic peptides are likely responsible for their high cell membrane permeability. Thus, we require the ability to predict complete structural ensembles for cyclic peptides, including the majority of cyclic peptides that have broad structural ensembles, to significantly improve our ability to rationally design cyclic-peptide therapeutics. Here, we introduce the idea of using molecular dynamics simulation results to train machine learning models to enable efficient structure prediction for cyclic peptides. Using molecular dynamics simulation results for several hundred cyclic pentapeptides as the training datasets, we developed machine-learning models that can provide molecular dynamics simulation-quality predictions of structural ensembles for all the hundreds of thousands of sequences in the entire sequence space. The prediction for each individual cyclic peptide can be made using less than 1 second of computation time. Even for the most challenging classes of poorly structured cyclic peptides with broad conformational ensembles, our predictions were similar to those one would normally obtain only after running multiple days of explicit-solvent molecular dynamics simulations. The resulting method, termed StrEAMM (Structural Ensembles Achieved by Molecular Dynamics and Machine Learning), is the first technique capable of efficiently predicting complete structural ensembles of cyclic peptides without relying on additional molecular dynamics simulations, constituting a seven-order-of-magnitude improvement in speed while retaining the same accuracy as explicit-solvent simulations.

The StrEAMM method enables predicting the structural ensembles of cyclic peptides that adopt multiple conformations in solution.     

Ionization of the Conformers of cis Nanotubular Cyclic Peptides in the Gas Phase: Effect of Size and Conformation on Ionization

Cyclic peptides, because of their unique spatial conformations, simplicity, and limited conformational freedom, are widely used as model molecules for larger peptides in chemistry and biochemistry. In this work, the ionization energies and photoelectron spectra of different conformers of the cyclic peptides (n = 2–15) were calculated using the symmetry‐adapted cluster‐configuration interaction (SAC‐CI) method and D95 + (d,p) basis set in the gas phase. The calculated photoelectron spectra were used to study the electronic structures of the cyclic peptides. It was observed that the first ionization energy of the cyclic peptides decreases with the ring size, reaches a minimum, and then increases. In addition, the first ionization band of the cyclic peptides was assigned to the ionization of the lone electron pairs of the nitrogen atoms, although there are π electrons of the CO bond and the lone electron pairs of oxygen atoms in the structure of the peptides.     

Stereoselective Fluorination Alters the Geometry of a Cyclic Peptide: Exploration of Backbone‐Fluorinated Analogues of Unguisin A

New methods for enhancing the efficiency of peptide cyclization, and for fine‐tuning the conformations of cyclic peptides, are valuable from a drug development perspective. Herein stereoselective fluorination is investigated as a new strategy for achieving these goals. Four vicinal difluorinated analogues of the natural cyclic heptapeptide unguisin A have been efficiently synthesized. The analogues are found to adopt dramatically different secondary structures, controlled by the fluorine stereochemistry.     

Tork: Conformational analysis method for molecules and complexes

A conformational search method for organic molecules and bimolecular complexes is presented. The method, termed Tork, uses normal-mode analysis in bond-angle-torsion coordinates and focuses on a key subset of torsional coordinates to identify natural molecular motions that lead the initial conformation to new energy minima. New conformations are generated via distortion along these modes and their pairwise combinations, followed by energy minimization. For complexes, special treatment is accorded to the six coordinates that specify the position and orientation of one molecule relative to the other. Tests described here show that Tork is highly efficient for cyclic, acyclic, and mixed single molecules, as well as for host-guest complexes.     

Constraining Cyclic Peptides To Mimic Protein Structure Motifs

Many proteins exert their biological activities through small exposed surface regions called epitopes that are folded peptides of well‐defined three‐dimensional structures. Short synthetic peptide sequences corresponding to these bioactive protein surfaces do not form thermodynamically stable protein‐like structures in water. However, short peptides can be induced to fold into protein‐like bioactive conformations (strands, helices, turns) by cyclization, in conjunction with the use of other molecular constraints, that helps to fine‐tune three‐dimensional structure. Such constrained cyclic peptides can have protein‐like biological activities and potencies, enabling their uses as biological probes and leads to therapeutics, diagnostics and vaccines. This Review highlights examples of cyclic peptides that mimic three‐dimensional structures of strand, turn or helical segments of peptides and proteins, and identifies some additional restraints incorporated into natural product cyclic peptides and synthetic macrocyclic peptidomimetics that refine peptide structure and confer biological properties.     

Solvent-Enhanced Conformational Flexibility of Cyclic Tetrapeptides

Solvent and temperature can affect the structural properties of cyclic peptides by controlling their flexibility. Here, we investigate two cyclic peptides, featuring beta turns. Using temperature-dependent NMR and FT-IR, we observed a pronounced temperature effect on the conformation of the cyclic peptide D-1 in CHCl₃ but a much smaller effect in CH₃CN. Almost no effect was observed for its diastereomer L-1 within a similar temperature range and using the same solvents. With the aid of Replica Exchange Molecular Dynamics simulations and Quantum Mechanics/Molecular Mechanics calculations, we were able to explain this behavior based on the increased flexibility of D-1 (in CHCl₃) in terms of intramolecular hydrogen bonding. The largest temperature dependence is observed for D - 1 in CHCl₃, while the temperature effect is less pronounced for L-1 in CHCl₃ and for both peptides in CH₃CN. This work provides new insights into the role of the environment and temperature on the conformations of cyclic peptides.     

N-methylated cyclic pentaalanine peptides as template structures

The N-methylation of cyclic peptides can be used to modify the activity and/or selectivity of biologically active peptides. As N-methylation introduces different flexibility and lipophilicity, it can also improve the bioavailability (the ADMET profile). To search for conformationally constrained cyclic peptides, a library of 30 different N-methylated peptides with the basic sequence cyclo(-D-Ala-L-Ala4-) was synthesized. Based on the NMR analysis, seven of these peptides exhibited single conformations (>98%). The structural features of these peptides were determined by a combination of NMR and distance geometry and then further refined by molecular dynamics simulations in an explicit DMSO solvent box. The structures provided from these efforts can now serve as templates for the rational design of cyclic pentapeptides with a distinct backbone conformation or for "spatial screening" to explore the bioactive conformation of medically important peptide systems.     

Synthesis of reversible cyclic peptides

A novel approach for the synthesis of cyclic peptides that can exist in either linear or cyclized conformations is described. Synthesis of the peptides was achieved via a modified solid phase methodology. The reversible linear/cyclized (i.e., open/closed) states are controlled via the reduction/oxidation of a disulfide bond incorporated into the backbone of the peptide chain.     

Quantum chemical study of cyclic dipeptides

The preferred conformations of cyclic dipeptides were first studied systemically using the density functional theory (DFT) B3LYP method at the 6‐31G(d) level. The structural characteristics of cyclic dipeptides were revealed, most of which have not been confirmed until now. Our studies showed that the six‐member main circles of cyclic dipeptides composed of natural L ‐amino acid residues appeared as boat conformations. The important factors that influence conformations of cyclic dipeptides, such as molecular total energy, nuclear repulsion energy, molecular orbit, spatial effects, and reactive mechanism, are discussed in detail. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Dissociation behavior of doubly-charged tryptic peptides: correlation of gas-phase cleavage abundance with ramachandran plots

Analysis of fragmentation patterns from 5654 unique doubly charged tryptic peptides is obtained. Great variability of average relative abundance of bond cleavage is found between different amino acid combinations. There exist similarities as well as differences between b and y ions. Strong enhancement or suppression of cleavage gives insight into possible chemical interactions at reactive conformations formed by preferred phi-psi angles.     

Vibrational Spectroscopy and Conformational Structure of Protonated Polyalanine Peptides Isolated in the Gas Phase

The conformational structures of protonated polyalanine peptides, Ala(n)H(+), have been investigated in the gas phase for n = 3, 4, 5, and 7 using a combination of resonant-infrared multiphoton dissociation (R-IRMPD) spectroscopy in the NH and OH stretch regions and quantum chemical calculations. Agreement between theoretical IR and experimental R-IRMPD spectral features has enabled the assignment of specific hydrogen-bonded conformational motifs in the short protonated peptides and revealed their conformational evolution under elevated-temperature conditions, as a function of increasing chain length. The shortest peptide, Ala(3)H(+), adopts a mixture of extended and cyclic chain conformations, protonated, respectively, at a backbone carbonyl or the N-terminus. The longer peptides adopt folded, cyclic, and globular charge-solvated conformations protonated at the N-terminus, consistent with previous ion-mobility studies. The longest peptide, Ala(7)H(+), adopts a globular conformation with the N-terminus completely charge-solvated, demonstrating the emergence of "physiologically relevant" intramolecular interactions in the peptide backbone. The computed conformational relative free energies highlight the importance of entropic contributions in these peptides.     

Helix and hairpin nucleation in short peptides using centrally positioned conformationally constrained dipeptide segments

The effect of incorporation of a centrally positioned Ac(6)c-Xxx segment where Xxx = (L)Val/(D)Val into a host oligopeptide composed of l-amino acid residues has been investigated. Studies of four designed octapeptides Boc-Leu-Phe-Val-Ac(6)c-Xxx-Leu-Phe-Val-OMe (Xxx = (D)Val 1, (L)Val 2) Boc-Leu-Val-Val-Ac(6)c-Xxx-Leu-Val-Val-OMe (Xxx = (D)Val 3, (L)Val 4) are reported. Diagnostic nuclear Overhouse effects characteristic of hairpin conformations are observed for Xxx = (D)Val peptides (1 and 3) while continuous helical conformation characterized by sequential N(i)H ? N(i+1)H NOEs are favored for Xxx = (L)Val peptides (2 and 4) in methanol solutions. Temperature co-efficient of NH chemical shifts are in agreement with distinctly different conformational preferences upon changing the configuration of the residue at position 5. Crystal structures of peptides 2 and 4 (Xxx = (L)Val) establish helical conformations in the solid state, in agreement with the structures deduced from NMR data. The results support the design principle that centrally positioned type I β-turns may be used to nucleate helices in short peptides, while type I'β-turns can facilitate folding into β-hairpins.     

Design and Synthesis of Calix[4] arene-Constrained Cyclopeptide

There have been great continuing interests in cyclic peptides in the past two decades. Apart from being useful tools for identifying the functional conformations of bioactive peptides, and guiding the rational design of peptidomimetic drugs, cyclic peptides serve as templates in the de novo design^[1] of artificial proteins and as models^[2] for the study of prepefence in protein secondary structure. They also play an important role in ion transport across biological membranes,^[3] and can self-assemble size-adjustable nanotubes.^[4] However, study on their molecular recognitions for ions^[5] and neutral molecules, especially for organic compounds,^[6,7] which are believed to be one of the most attractive properties, were hampered by their considerable large degree of the freedom of the cavities.     

The molecular mechanics of valinomycin. I. Energy minimization calculations on the uncomplexed ionophore

We have used energy minimization calculations to study a number of conformations of uncomplexed valinomycin. In certain cases, x-ray diffraction atomic coordinates were used directly as input coordinates, while in other cases, conformations were found by altering the x-ray coordinates prior to minimization. Five calculated conformations are reported along with their relative energies. The conformation found theoretically to be the most stable is in agreement with earlier, cruder calculations, but does not correspond to the predominant conformation observed in nonpolar solvents. A possible rationale is presented.     

Application and Structural Analysis of Triazole-Bridged Disulfide Mimetics in Cyclic Peptides

Ruthenium-catalysed azide–alkyne cycloaddition (RuAAC) provides access to 1,5-disubstituted 1,2,3-triazole motifs in peptide engineering applications. However, investigation of this motif as a disulfide mimetic in cyclic peptides has been limited, and the structural consequences remain to be studied. We report synthetic strategies to install various triazole linkages into cyclic peptides through backbone cyclisation and RuAAC cross-linking reactions. These linkages were evaluated in four serine protease inhibitors based on sunflower trypsin inhibitor-1. NMR and X-ray crystallography revealed exceptional consensus of bridging distance and backbone conformations (RMSD<0.5 Å) of the triazole linkages compared to the parent disulfide molecules. The triazole-bridged peptides also displayed superior half-lives in liver S9 stability assays compared to disulfide-bridged peptides. This work establishes a foundation for the application of 1,5-disubstituted 1,2,3-triazoles as disulfide mimetics.     

Disulfide Click Reaction for Stapling of S-terminal Peptides

A disulfide click strategy is disclosed for stapling to enhance the metabolic stability and cellular permeability of therapeutic peptides. A 17-membered library of stapling reagents with adjustable lengths and angles was established for rapid double/triple click reactions, bridging S-terminal peptides from 3 to 18 amino acid residues to provide 18- to 48-membered macrocyclic peptides under biocompatible conditions. The constrained peptides exhibited enhanced anti-HCT-116 activity with a locked α-helical conformation (IC₅₀=6.81 μM vs. biological incompetence for acyclic linear peptides), which could be unstapled for rehabilitation of the native peptides under the assistance of tris(2-carboxyethyl)phosphine (TCEP). This protocol assembles linear peptides into cyclic peptides controllably to retain the diverse three-dimensional conformations, enabling their cellular uptake followed by release of the disulfides for peptide delivery.     

β-Loop, γ-loop,and helical peptide conformations in cyclopeptides containing a steroidal pseudo-amino acid

The steroidal pseudo-amino acids 3ã-amino-5β-cholan-24-oic acid ( 2a ), 12ã-acetoxy-3ã-ammonia-5β-cholan-24-oic acid ( 2b ), and 7ã,12ã-diacetoxy-3ã-amino-5β-cholan-24-oic acid ( 2c ) are used as rigid spacers in the backbone of the cyclic peptides cyclo(– 2a –Phe-Phe–)₂ ( 1a ), cyclo(– 2b –Phe-Phe–)₂ ( 1b ), and cyclo(–2c-Phe-Phe–)₂ ( 1c ). A homogeneous β-loop conformation is found in the peptide chains of 1a and 1b , while 1c exists as a mixture of ã-helical and γ-loop conformations. The structure and homogeneity of the conformations are established by several NMR techniques and are supported by molecular-dynamics calculations. The peptide conformations depend on the distance and attraction of the two large and lipophilic steroidal parts of the cyclic molecules.