Synthesis and conformational study of a cyclic hexapeptide analog of somatostatin containing dehydrophenylalanine

De novo design of α,β-didehydrophenylalanine containing peptides: from models to applications

The de novo design of peptides and proteins has emerged as an approach for investigating protein structure and function. The success relies heavily on the ability to design relatively short peptides that can adopt stable secondary structures. To this end, substitution with α,β-dehydroamino acids, especially α,β-didehydrophenylalanine (ΔPhe or ΔF) has blossomed in manifold directions, providing a rich diversity of well-defined structural motifs. Introduction of α,β-didehydrophenylalanine induces β-bends in small and 3(10)-helices in longer peptide sequences. Most favorable conformation of ΔF residues are (φ,ψ) ∼(60°, 30°), (-60°, -30°), (-60°, 150°), and (60°, -150°). These features have been exploited in designing helix-turn-helix, helical bundle arrangements, and glycine zipper type super secondary structural motifs. The unusual capability of α,β-didehydrophenylalanine ring to form a variety of multicentered interactions (N-H…O, C-H…O, C-H…π, and N-H…π) suggests its possible exploitation for future de novo design of supramolecular structures. This work has now been extended to the de novo design of peptides with antibiotic, antifibrillization activity, etc. More recently, self-assembling properties of small dehydropeptides have been explored. This review focuses primarily on the structural and functional behavior of α,β-didehydrophenylalanine containing peptides.

Synthesis, crystal structure and molecular conformation of Nα-Boc-l-leucyl-(Z)-β-(3-pyridyl)-α,β- dehydroalanyl-l-leucine methyl ester*

A protected tridehydropeptide containing (Z)-beta-(3-pyridyl)-alpha,beta-dehydroalanine (Delta(Z)3Pal) residue, Boc-Leu-Delta(Z)3Pal-Leu-OMe (1), was synthesized via Erlenmeyer azlactone method. X-ray crystallographic analysis revealed that the peptide 1 adopts an extended conformation, which is similar to that of a Delta(Z)Phe analog, Boc-Leu-Delta(Z)Phe-Leu-OMe (2).

Structure-based design of a novel peptide inhibitor of HIV-1 integrase: a computer modeling approach

The insertion of viral DNA into the host chromosome is an essential step in the replication of HIV-1, and is carried out by an enzyme, HIV-1 integrase (IN). Since the latter has no human cellular counterpart, it is an attractive target for antiviral drug design. Several IN inhibitors having activities in the micromolar range have been reported to date. However, no clinically useful inhibitors have yet been developed. Recently reported diketo acids represent a novel and selective class of IN inhibitors. These are the only class which appear to selectively target integrase and two of the inhibitors, L-708,906 and L-731,988, are the most potent inhibitors of preintegration complexes described to date. The X-ray crystal structure of the IN catalytic domain complexed with a diketo acid derivative inhibitor, 5CITEP, has recently been determined. Although the structure is of great value as a platform for drug design, experimental data suggest that crystal packing effects influence the observed inhibitor position. This has been confirmed by computational docking studies using the latest version (3.0) of the AutoDock program, which has been shown to give results largely consistent with available experimental data. Using AutoDock 3.0 and SYBYL6.6 we have modeled the complexes of IN with the diketo acid inhibitors so as to identify the enzyme binding site. In the quest for novel, potent and selective small molecule inhibitors, we present here a new approach to peptide inhibitor design using a, b- unsaturated (dehydro) residues, which confer a unique conformation on a peptide sequence. Based on the above models, we selected a tetrapeptide sequence containing a dehydro-Phe residue, which was found to have an open conformation as ascertained from its X-ray crystal structure. Docking results on this peptide led us to propose a modification at the C-terminal end. The modified peptide was found to dock in a similar position as the diketo acid inhibitors and was predicted to have a comparable potency.

A peptide inhibitor of HIV-1 reverse transcriptase using alpha,beta-dehydro residues: a structure-based computer model

HIV-1 reverse transcriptase (RT) is a key enzyme involved in the replication of the virus and is a potential target for therapeutic intervention following infection. Several drugs that inhibit the enzyme from acting have been discovered. These include nucleoside-analogue inhibitors such as AZT (zidovudine), ddI and ddC, and non-nucleoside inhibitors such as nevirapine and delavirdine. All of them, however have been found to be of limited clinical utility because the RT becomes rapidly resistant to them on account of point mutations in the enzyme. One way to partly overcome this limitation is to design an inhibitor that has interactions mainly with the backbone and the conserved residues of RT. Using a rational drug-design approach based on the high resolution X-ray crystal structure of the RT-nevirapine complex (1), and the specific design principles of peptides containing dehydro-Alanine (deltaAla) generated by our theoretical calculations, we present here the design of a peptide inhibitor of RT. Energy minimization and molecular modeling of the interaction of the designed pentapeptide with the nevirapine-binding site indicate that the inhibitor has 60% of its interactions with the conserved regions of RT as compared to 30% in the case of nevirapine, thus making it much less sensitive to mutations in the enzyme.

A proteinase K inhibitor using alpha,beta-unsaturated (dehydro) residues: a presumptive model

Enzymes of the subtilisin family, of which proteinase K is a member, have been studied extensively on account of their numerous biological applications. Specific inhibitors of the proteinases are of immense importance in regulating their activity so as to protect the cells against uncontrolled proteolysis. Using the specific design principles of peptides containing dehydro-Alanine (deltaAla), generated by our theoretical calculations, we present here the design of an inhibitor of proteinase K. Energy minimization and molecular modeling of the interaction of the designed tetrapeptide with the recognition site of proteinase K indicate that it is an effective inhibitor.

Predicted conformation of poly(dehydroalanine): a preference for turns

Repetitive conformations of poly(dehydroalanine) were studied using molecular mechanics. An exhaustive search of the conformational space was carried out on a delta Ala octapeptide model, using the AMBER force field and the delta Ala parameters of Alagona et al [26], under three dielectric conditions, epsilon = 1 (vacuum), epsilon = r and epsilon = 4r (solvent). In all cases, two major groups of low-energy conformers were found, one corresponding to a regular 3/10 helix or type III turn, the other to an irregular conformation, phi = -157 to -170 degrees, psi = -1 to 15 degrees which however can be found in the i + 2 position of gamma-turns. The data confirm that delta Ala may induce turn-like structures in peptides and also indicate that it may confer flexibility to the peptide chain.

Solution structure of peptides containing two dehydro-phenylalanine residues: a CD investigation

The peptides Ac-delta Phe-Ala-delta Phe-NH-Me (1), Ac-delta Phe-Val-delta Phe-NH-Me (2), Ac-delta Phe-Gly-delta Phe-Ala-OMe (3), and Boc-Ala-delta Phe-Gly-delta Phe-Ala-OMe (4), containing two dehydro-phenylalanine (delta Phe) residues, were synthesized and the solution structure investigated in various solvents. The nmr and CD measurements indicate that all the dehydropeptides examined adopt 3(10)-helical conformations in solution. The tripeptides 1 and 2 exhibited an intense negative CD exciton couplet, which was assigned to the right-handed screw sense, while the tetrapeptide 3 displayed a CD couplet having opposite sign, which was assigned to the left-handed helical sense. In the pentapeptide 4 the sense of the helix was found to vary with solvent and temperature, as demonstrated by the sign reversal of the CD spectrum. The right-handed sense dominates in hexafluoro-2-propanol, whereas a left-handed helix prevails in chloroform, acetonitrile and methanol. A crucial role for this behavior is likely to be played by the two alanine residues positioned respectively at the head and tail of the sequence, which favor conformations having opposite screw senses.

Crystal and molecular structure of the dehydropeptide Ac-delta Phe-Val-delta Phe-NH-Me

The dehydropeptide Ac-delta Phe-L-Val-delta Phe-NH-Me, containing two dehydrophenylalanine (delta Phe) residues, crystallizes from methanol/water in space group P212121, with a = 12.622 (1), b = 12.979 (1), and c = 15.733 (1) A. In the solid state, the molecular structure is characterized by the presence of two intramolecular hydrogen bonds which form two consecutive beta-bends. The (phi, psi) torsion angles of the three residues are very similar and close to the standard values of type III beta-bends, so the molecular conformation corresponds to an incipient right-handed 3(10)-helix, only slightly distorted. In the crystal, the molecules are linked by head-to-tail hydrogen bonds, thus forming continuous helical columns packed in antiparallel mode. There are no lateral hydrogen bonds; the only interactions are hydrophobic contacts between the apolar side chains of neighboring helical columns.

Crystal and molecular structure of Boc-D-Ala-delta Phe-Gly-delta Phe- D-Ala-OMe: a 3 10-helical dehydropeptide

The crystal and molecular structure of the pentapeptide Boc-D-Ala-delta Phe-Gly-delta Phe-D-Ala-OMe, containing two dehydrophenylalanine residues, was determined by x-ray diffraction. The molecule crystallizes in the orthorombic P2(1)2(1)2(1) space group, with a = 10.439(3), b = 15.319(3) and c = 21.099(4) A. In the solid state, the conformation of the pentapeptide is characterized by the presence of two type III' beta-turns. Thus the peptide assumes a left-handed 3(10-helical conformation, the left sense being due to the D configuration of the alanine residues. The two unsaturated residues are located in the (i + 1) position of the first beta-turn and in the (i + 2) position of the second beta-turn, respectively. In the crystal, the helical molecules are linked head to tail by hydrogen bonds. Lateral hydrogen bonds are also formed between molecules related by a twofold screw symmetry. This gives rise to a typical mode of packing characterized by infinite helical "chains,' similar to the packing found in other oligopeptides that adopt a 3(10)-helical structure.

Conformational characteristics of peptides containing alpha, beta-dehydroamino acid residues

The structural preferences of synthetic peptides containing alpha, beta-dehydroamino acid residues, as determined by theoretical studies, x-ray diffraction analyses, and spectroscopic studies, are reviewed. The role of delta ZPhe residues in stabilizing type II beta-turn structures in small peptides and in nucleating helical structure in longer peptides is exemplified by several crystal as well as solution structural studies. From the few studies reported so far it appears that delta ZLeu influences the peptide backbone, much like the delta ZPhe residue, whereas delta Ala prefers the extended conformation, suggesting that the nature of beta substituents might influence the conformation restriction behavior of the dehydroresidues. Conformational studies on synthetic peptides containing delta E, delta ZAbu, and delta Val have also been described.