N-Methyl peptides

Secondary structure formation in N-substituted peptides

A systematic conformational analysis on several model peptides with N-substituted amino acids was performed on the basis of ab initio MO theory at the HF/6-31G* and HF/3-21G levels with inclusion of solvation effects to study the influence of N-substitution on the formation of typically secondary structural elements, e.g. beta sheets, helices and turns. The conformational flexibility of some structures was examined by means of molecular dynamics simulations in the gas phase and in solution. The results show a restriction of the conformational flexibility of the peptide chain after introduction of an N-substituted amino acid. N-substitution makes beta sheet formation more difficult. Several consecutive N-substituted amino acids in a sequence lead to conformers different from those found on the energy hypersurface of the corresponding N-unsubstituted peptides. There is a strong tendency to form periodically helical conformations, e.g. the polyglycine II or the alpha helix, which can be extended over several N-substituted amino acid residues. As long as 1<--4 hydrogen bond formation remains possible, the major types of beta turns can be formed with a distinct preference for the betaII and betaVIa turns. The betaI turn in particular is considerably destabilized.

Aza-peptides. II. X-ray structures of aza-alanine and aza-asparagine-containing peptides

In order to determine the structural consequences of the N alpha/C alpha H exchange in aza-peptides, we have solved the crystal molecular structures of some derivatives containing the aza-analogue of asparagine [Z-AzAsn(Me)-NMe2 (1), Z-AzAsn(Me)-Pro-NHiPr (2) and Piv-Pro-AzAsn(Me)-NHiPr (5)], aspartic acid [Z-AzAsp(OEt)-Pro-NHiPr (3) and alanine (Boc-AzAla-Pro-NHiPr (4)], by using X-ray diffraction. They reveal that the alpha-nitrogen accommodates a pyramidal (1-4) or planar (5) structure depending on the sequence. When pyramidal, the alpha-nitrogen assumes the R (D-like) chirality. All of the derivatives but 1 adopt either a beta 1-folded (2-4) or beta n-folded (5) structure in which the (AzAsn)N3H bond is intramolecularly hydrogen-bonded to the alpha-nitrogen.

Folded structures in protonated reduced dipeptides

Reduced dipeptides with the general formula RCO-Xaa-rXbb-N+HR'R" (rXbb, reduced analogue of residue Xbb: NH-C alpha HR1-CrH2) are shown to adopt a folded conformation in solution and in the solid state. The protonated reduced amide bond is an active proton donor capable of interacting with a peptide carbonyl to give a strong hydrogen bond topologically equivalent to the i+2 or i+3-->i interaction. The resulting conformation is similar to the y- or beta-turn structure found in peptides and proteins.

A unique phenylalanine-containing lipopeptide isolated from a rough-colony variant of Mycobacterium avium

Previous investigations have suggested that the biosynthesis of the Mycobacterium avium serovar-specific glycopeptidolipid antigens involves initial steps that include the participation of lipopeptides. The prevailing assumption is that subsequent glycosylation of those lipopeptides results in the fully glycosylated form of the glycopeptidolipid components. In an effort to identify potential precursors in the biosynthetic pathway of glycopeptidolipid components, we have identified a unique lipopeptide from an M. avium rough variant (MAC702) that was isolated from a patient suffering from a chronic M. avium lung infection. Upon examination it was revealed that although the total lipid extract from MAC702 lacked serovar-specific glycopeptidolipid antigens, it did contain a unique lipopeptide, possessing some amino acids identical to those found in the serovar-specific glycopeptidolipid antigens. Initial examination of acid-hydrolyzed samples of the lipopeptide (lipopeptide-I) revealed the presence of phenylalanine, alanine, and isoleucine, but no carbohydrate. Subsequent mass spectrometric and 1H-NMR and 1H-13C-NMR correlation spectroscopy analysis confirmed the initial results and also revealed the presence of N-methylisoleucine. The following structure for lipopeptide-I was proposed: fatty acyl (C19 or C17)-Phe-N-methyl-Ile-Ile-Phe-Ala-Ile-Ala-Phe. Lipopeptide-I is unlike any heretofore identified compound, however, it does have similar features to lipopeptides previously reported in mycobacteria and fungi. Although its structure does not verify that it is a direct precursor in glycopeptidolipid biosynthesis, the presence of certain components in lipopeptide-I indicate that it may share at least some pathways associated with the biosynthesis of the M. avium serovar-specific glycopeptidolipids.

Peptides and peptoids--a quantum chemical structure comparison

Peptoids represent a very interesting structure alternative to peptides. Based on ab initio MO theory employing the 6-31G* and 3-21G basis sets and considering correlation energy, a systematic structure comparison between the basic structure units of peptoids and peptides is performed. The calculations show three minimum conformations denoted as C7 beta, alpha D, and alpha that do not correspond to conformers on the peptide potential energy hypersurface. The possibility of cis peptide bonds in the peptoids was examined. The solvent influence on the structure was estimated by means of various quantum chemical continuum models.

Peptides as active probes

The use of peptides as probes of peptide binding sites of neuropeptide receptors, and of peptidases and proteases is discussed. The rapidly expanding use of peptide antigens as probes of protein structure and valuable diagnostics and vaccines is described. We also discuss the use of synthetic peptide motifs in studies on the molecular details of protein-protein and protein-nucleic acid interactions. Covalently modified peptides such as phosphopeptides exemplifies the use of synthetic peptides in the study of posttranslational modifications of proteins.

A free-energy simulation study of a bacterial collagenase inhibitor

The cis-trans conformational isomerisation of the N-methylated peptide bond of a bacterial collagenases peptide inhibitor (HS-CH2-CH2-CO-Pro-NMe-Ala) has been investigated by molecular dynamics simulations, energy minimisations and free-energy simulations in presence of solvent molecules. The free-energy difference between the cis and trans forms obtained by the thermodynamics integration method is equal to 0.95 kcal/mol in favour of the trans form, in accord with the experimental result. The main contribution to this free-energy difference comes from solute-water electrostatic interactions. Interestingly, we show that the number of interactions between water molecules and the oxygen atoms of the inhibitor is larger in the trans form than in the cis. Thus the organisation of water molecules around the inhibitor appears crucial in determining the population of the cis and trans conformers.

Conformational analysis of CCK-B agonists using 1H-NMR and restrained molecular dynamics: comparison of biologically active Boc-Trp-(N-Me) Nle-Asp-Phe-NH2 and inactive Boc-Trp-(N-Me)Phe-Asp-Phe-NH2

The tetrapeptide Boc-Trp-(N-Me)Nle-Asp-Phe-NH2 is a potent CCK-B agonist. Replacement in this analogue of the norleucine residue by a phenylalanine, to yield Boc-Trp-(N-Me) Phe-Asp-Phe-NH2, led to a 740-fold decrease in affinity whereas the same decrease in affinity was not observed in their nonmethylated counterparts. In order to ascertain the conformational preferences of these two N-methylated tetrapeptides, a study by two-dimensional (2D) nmr spectroscopy and molecular modeling was undertaken. The solution conformation of the two peptides was examined by 1H-nmr in a d6-DMSO/H2O (80:20) mixture. A cis-trans equilibrium, induced by N-methylation, was observed for both analogues, and the proton spectra of the two rotamers were fully characterized in each case. 1H-1H distance constraints, derived from 2D nuclear Overhauser effect spectroscopy and rotating frame nuclear Overhauser effect spectroscopy experiments, were used as inputs for subsequent restrained molecular dynamics simulations. Comparisons of the nmr and molecular modeling data point toward distinct conformational preferences for these two peptides with an opposite spatial orientation of the Trp residue, and could explain the large difference in their biological activities. Furthermore, the tridimensional structure of Boc-Trp-(N-Me)Nle-Asp-Phe-NH2 could serve as a model for the design of nonpeptide CCK-B agonists.

New method for the synthesis of N-methyl amino acids containing peptides by reductive methylation of amino groups on the solid phase

Primary amino groups on the model peptide Xaa-Ala-Pro-Lys(ClZ)-Tyr(2BrZ), synthesized on a p-methylbenzhydryl amine resin with conventional Boc/benzyl protective group strategy, were reacted with 4,4'-dimethoxydityl chloride in dichloromethane, resulting in the introduction of the dimethoxydityl group, which is an acid-labile N-alkyl type of protective group. The secondary amino groups thereby formed can be methylated by treating the peptide-resin with formaldehyde and sodium cyanoborohydride in N,N-dimethylformamide. After the removal of the dimethoxydityl group with trifluoroacetic acid, the resulting N-methylated amino acid residues with a free secondary amino groups are accessible for acylation with the next activated Boc amino acid. With this method majority of the 20 common amino acids can be monomethylated directly on the resin and, in most cases, with very low levels of the side reactions. In the cases where the complete methylation is difficult to achieve, the remaining primary amino groups can be selectively acylated in the presence of secondary amino groups with trimethylacetic acid 1-hydroxybenzotriazole ester. The method provides a convenient general route to synthesize N-methylated derivatives of most of the occurring and synthetic amino acids.

Conformational analysis of mu-selective [D-Ala2,MePhe4]enkephalins

The conformational space of the potent mu-selective opioids [D-Ala2,MePhe4,Gly-ol5]enkephalin (DAGO) and [D-Ala2,MePhe4,Met(O)-ol5]enkephalin (FK 33-824) has been analyzed by 1H-NMR spectroscopy and theoretical calculations involving systematic conformational searching and energy minimizations. A cis-trans equilibrium of the Gly3-MePhe4 amide bond is induced by the N-methyl group, and the more energetically favoured trans isomer is proposed as the biologically relevant form. A compact interaction between the side chains of Tyr1 and D-Ala2 was demonstrated by NOE and ROE effects in both peptides in D2O and DMSO-d6, further supported by shielding of the D-Ala2 methyl protons in both solvents. Analysis of coupling constants, NOE and ROE data indicated significant restriction of the conformational freedom of the MePhe4 side-chain for both peptides in the two solvents. The NMR results and theoretical calculations point towards folded low energy conformations characterized by a beta II-type turn around Gly3-MePhe4. For the trans isomer, a Tyr1-MePhe4 phenyl ring separation between 8.5 and 12.5 A was accompanied by proximity between the D-Ala2 side chain and the C-terminal in low energy conformations. The results are in good agreement with available data on related active enkephalins. The conformational effects induced by simultaneous incorporation of D-Ala2 and MePhe4 in enkephalins is discussed in the light of the enhanced mu-opioid receptor selectivity and activity of these peptides.

Peptide inhibitors of E. collagenolyticum bacterial collagenase--effect of N-methylation. Consequences on biological activity and conformational properties

Peptide inhibitors of E. collagenolyticum bacterial collagenase, HS-CH2-CH2-CO-Pro-Yaa (Yaa = Ala, Leu, Nle), have been N-methylated at the Yaa position. The N-methylation slightly increases the inhibitory potency of the modified peptides as compared to the parent compounds. The conformational effects of the N-methylation have been investigated by both 1H 2D-NMR and molecular mechanics energy minimization. Three low-energy conformers have been predicted for the unmethylated parent compounds (Yaa = Ala, Leu, Nle). They are characterized by the psi value of the central proline residue: psi Pro = 150 degrees (trans' conformation), psi Pro = 70 degrees (C7 conformation) and psi Pro = -50 degrees (cis' conformation). The N-methylation has been found to strongly increase the energy of the C7 conformer and to a less extent the energy of the cis' conformer. This leaves the trans' conformation as the only low-energy conformer. The ROESY experiments have established that both the N-methyl peptides and the parent compounds adopt the same preferred backbone conformation in water solution, i.e. the trans' conformation. Based on these results, the activities of the N-methyl peptides are discussed and a possible conformation of the inhibitor in the bound state is proposed.

Conformationally constrained tachykinins: N-methylated analogues of neurokinin A

Limited conformational constraints have been introduced in the sequence of the C-terminal fragment of the peptide neurotransmitter neurokinin A by N-methylation of individual peptide bonds, and the biological activities of the peptides thus obtained were evaluated in order to assess the effect of such conformational constraint on receptor selectivity. The analogue methylated in position 7 shows enhanced selectivity toward NK-1 receptor.

1H-NMR studies of receptor-selective substance P analogues reveal distinct predominant conformations in DMSO-d6

Proton nmr parameters are reported for DMSO-d6 solutions of two receptor-selective substance P analogues: Ac[Arg6,Pro9]SP6-11, which is selective for the NK-1 (SP-P) receptor and [pGlu6,N-MePhe8]SP6-11, which selectively activates the NK-3 (SP-N) receptor. Full peak assignments of both analogues were obtained by COSY experiments. The chemical shifts, coupling constants, and temperature coefficients of amide proton chemical shifts as well as NOESY effects and calculated side-chain rotamer populations of Phe side chains are reported for both peptides. Analysis of coupling constants and temperature coefficients together with the nuclear Overhauser enhancement spectroscopy effects suggest that Ac[Arg6,Pro9]SP6-11 has a trans configuration about the Phe8-Pro9 amide bond and the preferred conformation of this analogue has a type I beta-turn. The nmr data for [pGlu6,N-MePhe8]SP6-11 suggest that this peptide exists as a mixture of cis-trans isomers in which the cis isomer can preferably adopt a type VI beta-turn conformation, and the trans isomer can adopt a gamma-turn conformation. There are indications that the two last turns are stabilized by a hydrogen bond between the syn carboxamide proton and the pGlu ring carbonyl.

Pseudopeptides and beta folding: x-ray structures compared with structures in solution

In order to restrain the flexibility of the peptide molecules and reduce their biodegradation, modifications of the main chain are now introduced in pseudopeptide analogues. Surprisingly, there is very little data on the conformational properties of these derivatives. We have examined pseudopeptide analogues of RCO-X-Y-NHR' model dipeptides in the depsi, N-methylated, reduced, retro, alpha, beta-dehydro, beta-amino acid, and hydrazino series, in the solid state by x-ray diffraction, and in solution by ir and 1H-nmr spectroscopy. This study provides us with accurate dimensions of the peptide surrogates, and gives some information on the conformational tendencies induced by these substitutions, with reference to those of the related dipeptide sequences.

Synthesis and conformational study in solution and in solid state of oligopeptides containing L-leucine and glycine

The synthesis and conformational studies of the oligopeptide N-tert.-butyloxycarbonyl-L-Leu-(L-Leu-Gly)n-OBzl (n = 1, 3, 5) and N-tert.-butyloxycarbonyl-(L-Leu-Gly)2-OBzl are described. The peptides were synthesized by stepwise and fragment condensation techniques using dicyclohexylcarbodiimide as the condensing agent in solution. The conformational study of the oligopeptides was carried out using CD, u.v. and i.r. spectra. The conformation in solution was examined in trifluoroethanol, hexafluoroisopropanol, hexafluoroacetone trihydrate, and methanol. CD spectra in trifluoroethanol exhibited a gradual variation with increasing peptide chain length. This can be interpreted as a formation of an ordered structure which is already present in the heptapeptide and, to a greater extent, in the undecapeptide. The results obtained from the CD profiles and i.r. spectra showed the presence of beta structure with antiparallel chains in the heptapeptide and undecapeptide. Finally, CD spectra revealed in trifluoroethanol-water solution the binding of Ca2+ to heptapeptide and undecapeptide together with a contemporaneous conformational change. This change is probably due to the formation of beta-turns. No change in the CD profiles was obtained by using Mg2+, K+, Na+, and Li+ ions instead of Ca2+.

Synthesis and biological activity of N-methylated analogues of neurokinin A

Limited conformational constraints have been introduced in the sequence of the C-terminal heptapeptide NKA(4-10) by N-methylation of individual peptide bonds and the biological activities of the peptides thus obtained were evaluated on three in vitro preparations sensitive and quite selective for each of the naturally-occurring neurokinins, in order to assess the effect of N-methylation on receptor selectivity. The analogue methylated in position 7, namely [MeVal7] NKA(4-10) shows some selectivity for the NK-P receptor, while none of the tested compounds appear to be selective for the NK-A receptor.