Enhancement of the T140-based pharmacophores leads to the development of more potent and bio-stable CXCR4 antagonists

A CXCR4 antagonistic peptide, T140, and its bio-stable analogs, such as Ac-TE14011, were previously developed. These peptides inhibit the entry of T cell line-tropic strains of HIV-1 (X4-HIV-1) into T cells. Herein, a series of TE14011 analogs having modifications in the N-terminal region were synthesized to develop effective compounds with increased biostability. Among these analogs, 4F-benzoyl-TE14011 (TF14013) showed the strongest anti-HIV activity derived from CXCR4-antagonism, suggesting that a 4-fluorobenzoyl moiety at the N-terminus of T140 analogs constitutes a novel T140-based pharmacophore for CXCR4 antagonists. Structure-activity relationship (SAR) studies on TE14011 analogs with N(alpha)-acylation by several benzoic acid derivatives have disclosed a significant relationship between the anti-HIV activity and the Hammett constant (sigma) of substituted benzoic acids. TF14013 was found to be stable in mouse serum, but not completely stable in rat liver homogenate due to deletion of the C-terminal Arg14-NH2 from the parent peptide. This biodegradation was completely suppressed by N-alkyl-amidation at the C-terminus. Taken together, the enhancement of the T140-based pharmacophores led to development of a novel CXCR4 antagonist, 4F-benzoyl-TE14011-Me (TF14013-Me), which has very high anti-HIV activity and increased biostability.     

Circular dichroism study of the carbohydrate-modified opioid peptides

The conformational preferences of enkephalins and the related glycoconjugates in which free or protected carbohydrate moieties were linked to the opioid peptides through an ether, ester or amide bond were investigated by circular dichroism spectroscopy in water, trifluoroethanol and water-trifluoroethanol mixtures. The analysis of the spectra revealed that the conformation of the enkephalin molecule is very sensitive to slight changes in the peptide structure around the C-terminal region. It was found that the type II beta-turn structures are populated in N-terminal tetrapeptide enkephalin fragment, while leucine-enkephalin amide feature a type I (III) beta-turn structure in solution. Incorporation of the sugar moiety into opioid peptide compound did not significantly influence the overall conformation of the peptide backbone, although minor intensity changes may reflect shifts in the population of the different turn systems. These small structural alterations can be responsible for the receptor-subtype selectivity of the various carbohydrate-modified enkephalin analogs.     

The ethylene group as a peptide bond mimicking unit: A theoretical conformational analysis

One of the features of the polypeptide backbone is that it represents a flexible chain that contains almost rigid CO? NH peptide bonds. One may try to substitute one or more such bonds by another relatively rigid unit to maintain the overall conformational properties of the backbone and at the same time modify some other properties of the molecule (“pseudopeptide”), such as the ability to form hydrogen bonds. By a detailed conformational analysis, it is shown that the carbon? carbon double bond is quite isosteric with the peptide bond and for this reason suitable for such a substitution. This is accomplished by applying molecular mechanics in calculation of the ?, ψ maps for pseudopeptide analogs of the N-acetyl-Ala-NHMe molecule. © 1993 John Wiley & Sons, Inc.     

Observation of noncovalent complexes between margatoxin and the Kv1.3 peptide ligands: A model investigation using ion-spray mass spectrometry

Margatoxin (MgTX), a 39 amino acid peptide present in the venom of the new world scorpion Centruroides margaritatus, is a potent inhibitor of the voltage-gated potassium channel (K_v1.3) in human peripheral T lymphocytes. Peptide analogs corresponding to the amino acid segments that are located at the rat K_v1.3 putative binding site for the ion channel blockers were synthesized. Gas phase noncovalent complexes of the synthetic analogs of the rat K_v1.3 peptide ligands with MgTX were detected using ion-spray mass spectrometry.     

Effect of chain length on the conformation and T cell recognition of synthetic hemagglutinin fragments

Circular dichroism and Fourier-transform infrared spectroscopies were used to compare the conformational mobility of 13-mer peptides covering the 317-329 region of the envelope protein hemagglutinin of human influenza A virus subtypes H1, H2 and H3 with that of their truncated deca- and nonapeptide analogs. These peptides were demonstrated to bind to the murine I-Ed major histocompatibility complex encoded class II and human HLA-B*2705 class I molecules. Despite the amino acid substitutions in the three 13-mer subtype sequences, no significant differences in the conformational properties could be shown. Deletion of the N-terminal three residues resulted in a shift to an increased alpha-helical conformer population in the 317-329 H1 peptide and the breakage of the 3(10) or weakly H-bonded (nascent) alpha-helix in the H2 and H3 peptides. The conformational change observed upon deletion did not influence the efficiency of I-Ed peptide interaction, however, the C-terminal Arg had a beneficial effect both on MHC class II and class I binding without causing any remarkable change in solution conformation.     

Micellar electrokinetic chromatography separations of dynorphin peptide analogs

Prodynorphin is a precursor that has multiple cleavage sites to release various dynorphin opioid peptides. The dynorphin analogs used in this study have 18 amino acid residues. A series of dynorphin-like peptides, differing by a single residue (alanine substitution) were assembled by Fmoc solid-phase procedures and purified by preparative high performance liquid chromatography (HPLC). Separation of the Ala-scan dynorphin analogs was investigated by micellar electrokinetic chromatography (MEKC) employing anionic, cationic and zwitterionic surfactants. The role of electrostatic and hydrophobic forces in analyte-surfactant interactions is discussed with respect to the observed elution patterns. Separation of all dynorphin analogs by MEKC using a zwitterionic surfactant shows this technique to be powerful for separating closely related peptide species. It also demonstrates the potential for using MEKC for the prescreening of peptide libraries to determine their biological activity toward specific receptors. Results from the separation of dynorphin analogs by free solution and ion-pairing capillary electrophoresis are also presented.     

Conformational preferences of an amyloidogenic peptide: IR spectroscopy of Ac-VQIVYK-NHMe

The (306)VQIVYK(311) sequence in the tau peptide is essential for the formation of intracellular amyloid fibrils related to Alzheimer's disease, where it forms interdigitating cross-beta-structures. The inherent conformational preferences of the capped hexapeptide Ac-VQIVYK-NHMe were characterized in the gas phase. IR/UV double-resonance spectroscopy of the peptide isolated in a cold molecular beam was used to probe the conformation of the neutral peptide. The influence of protonation at the lysine side chain was investigated at 298 K by characterizing the protonated peptide ion, Ac-VQIVYK(H(+))-NHMe, with IRMPD spectroscopy in the fingerprint and amide I/II band region in an FTICR mass spectrometer. The conformations for both neutral and protonated peptides were predicted by an extensive conformational search procedure followed by cluster analysis and then DFT calculations. Comparison of the experimental and computed IR spectra, with consideration of the relative energies, was used to assign the dominant conformations observed. The neutral peptide adopts a beta-hairpin-like conformation with two loosely extended peptide chains, demonstrating the preference of the sequence for extended beta-strand-like structures. In the protonated peptide, the lysine NH3(+) disrupts this extended conformation by binding to the backbone and induces a transition to a random-coil-like structure.     

Effect of poly(ethylene glycol) (PEG) spacers on the conformational properties of small peptides: a molecular dynamics study

Poly(ethylene glycol) (PEG) is used as an inert spacer in a wide range of biotechnological applications such as to display peptides and proteins on surfaces for diagnostic purposes. In such applications it is critical that the peptide is accessible to solvent and that the PEG does not affect the conformational properties of the peptide to which it is attached. Using molecular dynamics (MD) simulation techniques, we have investigated the influence of a commonly used PEG spacer on the conformation properties of a series of five peptides with differing physical-chemical properties (YGSLPQ, VFVVFV, GSGGSG, EEGEEG, and KKGKKG). The conformational properties of the peptides were compared (a) free in solution, (b) attached to a PEG-11 spacer in solution, and (c) constrained to a two-dimensional lattice via a (PEG-11)(3) spacer, mimicking a peptide displayed on a surface as used in microarray techniques. The simulations suggest that the PEG spacer has little effect on the conformational properties of small neutral peptides but has a significant effect on the conformational properties of small highly charged peptides. When constrained to a two-dimensional surface at peptide densities similar to those used experimentally, it was found that the peptides, in particular the polar and nonpolar peptides, aggregated strongly. The peptides also partitioned into the PEG layer. Potentially, this means that at high packing densities only a small fraction of the peptide attached to the surface would in fact be accessible to a potential interaction partner.     

13C NMR spectroscopic studies on the conformation during stepwise synthesis of peptides bound to solubilizing polymer supports

The C-13 {C-13-H-1} triple resonance technique allows constitutional and conformational studies on polypeptides bound to mono- and bi-functional solubilizing polyoxyethylene supports. High resolution shows distinct differences between random coil and α-helical conformations. This method is a valuable additional tool for control of the growing peptide during stepwise synthesis on soluble polymeric supports. Examples of partial sequences of the polypeptide antibiotic alamethicin and sequential analogs (Aib-Ala)_n demonstrate the applicability for peptide polyoxyethylene esters with mean molecular masses between 2000 and 10,000.     

A proposed bioactive conformation of Peptide T

The conformational profiles of Peptide T, (5–8)Peptide T, [Abu⁵](4–8)Peptide T and (4–8)Peptide T were computed independently to assess the geometrical characteristics of the bioactive conformation of Peptide T. The conformational profiles of the peptides were computed within the molecular mechanics framework using an effective dielectric constant of 80. The conformational space was thoroughly sampled using an iterative simulated annealing protocol. The bioactive conformation was assessed by pairwise cross comparisons of each of the unique low energy conformations found for each of the different analogs studied. After a putative bioactive conformation was selected, in order to further validate our hypothesis the conformational profile of the potent compound cyclo(Thr-Thr-Asn-Tyr-Thr-Asp) was computed and the putative bioactive conformation was found. The conformation exhibits a pseudo -turn involving the side chain of Thr⁵ and the carbonyl oxygen of Tyr⁷ forming a C12 ring.     

Conformational behaviour of the antineoplastic peptide dolastatin-10 and of two mutated derivatives

Summary The three-dimensional structure of dolastatin-10, an extremely potent cytostatic and antineoplastic peptide extracted from the mollusc Dolabella auricularia, has not yet been fully characterized in an experimental way. By means of a systematic conformational search of the natural peptide and of two mutated analogs, carried out both in vacuo and in aqueous solution, the present work allows to obtain insights into the conformational preferences of this remarkable compound. In addition, the ability to form intra- and intermolecular H-bonds as a function both of the sequence and of the conformation is discussed. The search for the best molecular conformations has been carried out using a molecular mechanics approach, based on the CVFF potential. Dolastatin-10 contains some unusual amino acids for which no experimental structural data are available. In order to check the reliability of the CVFF potential in predicting structures of such nonconventional amino acids, geometry optimizations have been carried out using the ab initio Hartree-Fock procedure. The CVFF parameterization is found to be adequate also for nonconventional amino acids.     

The Glu143 Residue Might Play a Significant Role in T20 Peptide Binding to HIV-1 Receptor gp41: An In Silico Study

Despite the enormous efforts made to develop other fusion inhibitors for HIV, the enfuvirtide (known as T20) peptide is the only approved HIV-1 inhibitory drug so far. Investigating the role of potential residues of the T20 peptide’s conformational dynamics could help us to understand the role of potential residues of the T20 peptide. We investigated T20 peptide conformation and binding interactions with the HIV-1 receptor (i.e., gp41) using MD simulations and docking techniques, respectively. Although the mutation of E143 into alanine decreased the flexibility of the E143A mutant, the conformational compactness of the mutant was increased. This suggests a potential role of E143 in the T20 peptide’s conformation. Interestingly, the free energy landscape showed a significant change in the wild-type T20 minimum, as the E143A mutant produced two observed minima. Finally, the docking results of T20 to the gp41 receptor showed a different binding interaction in comparison to the E143A mutant. This suggests that E143 residue can influence the binding interaction with the gp41 receptor. Overall, the E143 residue showed a significant role in conformation and binding to the HIV-1 receptor. These findings can be helpful in optimizing and developing HIV-1 inhibitor peptides.     

Theoretical conformational analysis of opiate peptides Leu-Enkephalin (H-Tyr-Gly-Gly-Phe-Leu-OH) and its two thioamide analogs (H-Tyr-Glyψ[CSNH]Gly-Phe-Leu-OH) and (H-Tyr-Gly-Glyψ[CSNH]Phe-Leu-OH)

In order to find informations on the native structure of the Leu-Enkephalin opiate peptide, the parent peptide and its two thioamide analogs (Thio-Gly2)Leu-Enkephalin and (Thio-Gly3)Leu-Enkephalin were studied by the theoretical method PEPSEA. This comparative conformational analysis showed that the active conformation is a β turn structure centered on Gly3 and Phe4. Moreover, this study showed also that the more active analog (Thio-Gly2)Leu-Enk has a lower tendency to adopt this structure. Consequently, its high activity can only be explained by its long lifetime due to its resistance to enzymatic hydrolysis, following the substitution of the amide linkage by the thioamide one. The weakly active analog (Thio-Gly3)Leu-Enk does not adopt this structure and prefers instead a β turn structure centered on Gly2 and Gly3. This study also confirmed the importance of the distances between the Tyr and Phe residues at positions 1 and 4, and that of the terminal Tyrosine N-H group which must be free of any intramolecular hydrogen bond in order to be available in the molecular recognition process.     

A 1,3-phenyl-linked hydantoin oligomer scaffold as a β-strand mimetic

A synthetic scaffold that mimics a peptide β-strand has been designed and synthesised based on a 1,3-phenyl-linked hydantoin oligomer. The conformational preferences of this oligomer were investigated using molecular modelling and solution NMR experiments and suggest a planar conformation that accurately mimics the i, i + 2 and i + 4 residues of a peptide β-strand.     

Sequence and modified group analysis on C-terminal modified analogs of endomorphin-2 using electrospray ionization-Fourier transform ion cyclotron resonance mass spectrometer

In this paper, a series of C-terminal modified analogs of endomorphin-2 is investigated using ESI-FT-ICR-MS. Some b, y″, a, and internal ions are found in the CID spectra and slight mass differ- ences between the calculated and observed results are obtained. Moreover, if the C-terminal modified group is t-butyloxy, it can lose butene through McLafferty rearrangement. FT-ICR MS shows its power in peptide sequencing successfully helping us obtain the structure of peptide analogs.     

Aggregation modes of the spin mono-labeled tylopeptin B and heptaibin peptaibiotics in frozen solutions of weak polarity as studied by PELDOR spectroscopy

The X band PELDOR spectroscopy was used to investigate the magnetic dipole-dipole interactions in glassy solutions of nitroxide mono-labeled tylopeptin B and heptaibin peptaibiotics at 77 K. Specifically, a study was performed of the tylopeptin B peptides labeled at either position 3, 8, or 13, denoted as T3, T8, and T13, respectively. The heptaibin analogs labeled at either position 2 or 14, denoted as H2 and H14, respectively, were also investigated. It was shown that in frozen glassy peptide solutions in methanol, the spin labels are randomly distributed over the solvent volume. This result points to the absence of specific dipolar interactions between the peptides under these conditions. However, peptide aggregation was detected in weakly polar methanol/toluene environments. To study the properties of the resulting aggregates, we examined the depth of modulation for the PELDOR traces as a function of the concentration of the peptides in solution and the distances between the spin labels in the aggregates. Based on the concentration dependencies, the number of peptide molecules in the aggregates was estimated. We find that this value ranges from 2 to 3, depending on the position of the spin label in the peptide sequence. The combined analysis of the distance spectra and the number of peptide molecules in the aggregates allows us to suggest that dimer formation is the prevailing mode of self-association. In the case of spin-labeled tylopeptin B, the molecules in the dimer are head-to-head oriented. In addition, the distance spectra of the aggregates show that the C-termini of the molecules in the tylopeptin B dimer are more mobile than the Ntermini. This phenomenon leads to an increase in the spread of the distances between the nitroxides as the label position is approaching the peptide C-terminus. For heptaibin, we show that two forms of dimerization (head-to-head and head-to-tail) occur. Finally, in addition to dimers, aggregates containing 3 or 4 peptide molecules, which give broad lines in the distance spectra, are seen in solution.     

Side-chain conformational space analysis (SCSA): A multi conformation-based QSAR approach for modeling and prediction of protein–peptide binding affinities

In this article, the concept of multi conformation-based quantitative structure-activity relationship (MCB-QSAR) is proposed, and based upon that, we describe a new approach called the side-chain conformational space analysis (SCSA) to model and predict protein-peptide binding affinities. In SCSA, multi-conformations (rather than traditional single-conformation) have received much attention, and the statistical average information on multi-conformations of side chains is determined using self-consistent mean field theory based upon side chain rotamer library. Thereby, enthalpy contributions (including electrostatic, steric, hydrophobic interaction and hydrogen bond) and conformational entropy effects to the binding are investigated in terms of occurrence probability of residue rotamers. Then, SCSA was applied into the dataset of 419 HLA-A 0201 binding peptides, and nonbonding contributions of each position in peptide ligands are well determined. For the peptides, the hydrogen bond and electrostatic interactions of the two ends are essential to the binding specificity, van der Waals and hydrophobic interactions of all the positions ensure strong binding affinity, and the loss of conformational entropy at anchor positions partially counteracts other favorable nonbonding effects.     

Single-Centre Model for the Active Site of α-Chymotrypsin

The polymer-bound heptapeptide H-Glu-His-Pro-Gly-Ser-Gly-PEGM was designed as a ‘single-centre model’ for the active site of α-chymotrypsin. The peptide was synthesized according to the general principles of the liquid-phase method for peptide synthesis, and its conformational properties were investigated by CD and IR spectroscopy in solution and in the solid state. In harmony with empirical prediction codes, experimental and theoretical conformational considerations, the peptide adopts a β-turn conformation stabilized by H-bonds involving the side chains of Glu, His, and Ser. The development of a H-bonded system similar to the active site of α-chymotrypsin leads to implications with respect to a possible catalytic activity of the model peptide.     

Structural and ITC Characterization of Peptide-Protein Binding: Thermodynamic Consequences of Cyclization Constraints,a Case Study on Vascular Endothelial Growth Factor Ligands

Macrocyclization constraints are widely used in the design of protein ligands to stabilize their bioactive conformation and increase their affinities. However, the resulting changes in binding entropy can be puzzling and uncorrelated to affinity gains. Here, the thermodynamic (Isothermal Titration Calorimetry) and structural (X-ray, NMR and CD) analysis of a complete series of lactam-bridged peptide ligands of the vascular endothelial growth factor, and their unconstrained analogs are reported. It is shown that differences in thermodynamics arise mainly from the folding energy of the peptide upon binding. The systematic reduction in conformational entropy penalty due to helix pre-organization can be counterbalanced by an unfavorable vibrational entropy change if the constraints are too rigid. The gain in configurational entropy partially escapes the enthalpy/entropy compensation and leads to an improvement in affinity. The precision of the analytical ITC method makes this study a possible benchmark for constrained peptides optimization.