Studies on amino acids and peptides VIII

Contemporary Applications of Thioamides and Methods for Their Synthesis

Thioamides are naturally occurring isosteres of amide bonds in which the chalcogen atom of the carbonyl is changed from oxygen to sulfur. This substitution gives rise to altered nucleophilicity and hydrogen bonding properties with importance for both chemical reactivity and non-covalent interactions. As such, thioamides have been introduced into biologically active compounds to achieve improved target affinity and/or stability towards hydrolytic enzymes but have also been applied as probes of protein and peptide folding and dynamics. Recently, a series of new methods have been developed for the synthesis of thioamides as well as their utilization in peptide chemistry. Further, novel strategies for the incorporation of thioamides into proteins have been developed, enabling both structural and functional studies to be performed. In this Review, we highlight the recent developments in the preparation of thioamides and their applications for peptide modification and study of protein function.

Opportunities and challenges in the synthesis of thioamidated peptides

Chemical modifications of peptides hold great promise for modulating their pharmacological properties. In the last few decades amide to thioamide substitution has been widely explored to modulate the conformation, non-covalent interactions, and proteolytic stability of peptides. Despite widespread utilization, there are some potential limitations including epimerization and degradation under basic and acidic conditions, respectively. In this chapter, we present the synthetic method to build thio-precursors, their site-specific incorporation onto a growing peptide chain, and troubleshooting during the elongation of thioamidated peptides. This highly efficient, rapid, and robust method can be used for positional scanning of the thioamide bond.

Thioamides in the collagen triple helix

To probe noncovalent interactions within the collagen triple helix, backbone amides were replaced with a thioamide isostere. This subtle substitution is the first in the collagen backbone that does not compromise thermostability. A triple helix with a thioamide as a hydrogen bond donor was found to be more stable than triple helices assembled from isomeric thiopeptides.

Microwave-assisted synthesis of potent PDE7 inhibitors containing a thienopyrimidin-4-amine scaffold

Thienopyrimidin-4-amines have been synthesized, evaluated and modelled as phosphodiesterase inhibitors.

Thionoglycine as a multifunctional spectroscopic reporter of screw-sense preference in helical foldamers

A single thionoglycine (glycine thioamide, -HNCH2C(=S)-) residue inserted into a peptide foldamer provides both a pair of germinal protons for use as a (1)H NMR stereochemical probe and a chromophore giving rise to a well defined Cotton effect in CD. Comparison of the response of these two features to a local helically chiral environment validates them as independent methods for quantifying the conformational screw-sense preference of a helical oligomer, in this case a peptide made of repeated Aib units. The sign of the Cotton effect provides a measure of the sign of the screw-sense preference, while both the chemical shift separation of the anisochronous signals of the glycine CH2 group and the magnitude of the Cotton effect give an estimate of the helicity excess of the oligomer. The thionoglycine unit is readily introduced synthetically by a thionation of a BocGlyAibOMe dipeptide.

Partial thioamide scan on the lipopeptaibiotic trichogin GA IV. Effects on folding and bioactivity

Backbone modification is a common chemical tool to control the conformation of linear peptides and to explore potentially useful effects on their biochemical and biophysical properties. The thioamide, ψ[CS-NH], group is a nearly isosteric structural mimic of the amide (peptide) functionality. In this paper, we describe the solution synthesis, chemical characterization, preferred conformation, and membrane and biological activities of three, carefully selected, peptide analogues of the lipopeptaibiotic [Leu¹¹-OMe] trichogin GA IV. In each analogue, a single thioamide replacement was incorporated. Sequence positions near the N-terminus, at the center, and near the C-terminus were investigated. Our results indicate that (i) a thioamide linkage is well tolerated in the overall helical conformation of the [Leu¹¹-OMe] lipopeptide analogue and (ii) this backbone modification is compatible with the preservation of its typical membrane leakage and antibiotic properties, although somewhat attenuated.

Direct Fmoc-chemistry-based solid-phase synthesis of peptidyl thioesters

Attachment of a growing peptide chain to a glycylaminomethyl resin via a thioglycinamide bond is compatible with Fmoc-chemistry solid-phase peptide synthesis. Subsequent S-alkylation of the thioamide gives a thioimide that, on treatment with aqueous trifluoroacetic acid, releases the peptide from the resin in the form of a C-terminal thioester.

Two-dimensional infrared spectroscopy of photoswitchable peptides

We present a detailed discussion of the complimentary fields of the application of two-dimensional infrared (2D-IR) spectroscopy in comparison with two-dimensional nuclear magnetic resonance (2D-NMR) spectroscopy. Transient 2D-IR (T2D-IR) spectroscopy of nonequilibrium ensembles is probably one of the most promising strengths of 2D-IR spectroscopy, as the possibilities of 2D-NMR spectroscopy are limited in this regime. T2D-IR spectroscopy uniquely combines ultrafast time resolution with microscopic structural resolution. In this article we summarize our recent efforts to investigate the ultrafast structural dynamics of small peptides, such as the unfolding of peptide secondary structure motifs. The work requires two ingredients: 2D-IR spectroscopy and the possibility of triggering a structural transition of a peptide on an ultrafast timescale using embedded or intrinsic photoswitches. Several photoswitches have been tested, and we discuss our progress in merging these two pathways of research.

Coexistence of Hydrogen-Bonded Loop and Extended Tetrapeptide Conformations

The conformations of a protected tetrathiopeptide have been analysed by isotope labelling and two-dimensional infrared spectroscopy (2D-IR). It has been found that Boc-Ala-Gly(=S)-Ala-Aib-OMe in acetonitrile, as well as its oxopeptide analogue, can adopt a hydrogen-bonded loop conformation in coexistence with less restricted structures. The two types of conformations interconvert too quickly to be resolved on the nuclear magnetic resonance (NMR) timescale, but give rise to different cross peaks in two-dimensional infrared spectra. The hydrogen bond between the Boc terminal group and the amide proton of Aib can be broken by photoisomerisation of the thioamide bond.

cis/trans Photoisomerization of Secondary Thiopeptide Bonds

The reversible cis/trans photoisomerization of secondary thiopeptide bonds has been systematically studied with UV-visible absorption, capillary electrophoresis, 1H NMR spectroscopy, and circular dichroism methods. It was found that the concentration of the cis conformers could be increased from less than 1 % in the thermal equilibrated solution to up to 20 % in the photostationary state. The rotational barriers of the thiopeptide bond and the pH dependence of the isomerization rates were also studied. The quantum yields of the trans-->cis and the cis-->trans processes were determined from photokinetic analysis.

Synthesis, X-ray crystallographic structures of thio substituted N-acetyl N'-methylamide alanine and evaluation of sp sulfur parameters of the CFF91 force field

Acetyl thioalanine N-methyl (Ac-Alat-NHMe) and thioacetyl alanine N-methyl (Act-Ala-NHMe) were synthesized, crystallized and their X-ray diffraction structures determined for the first time. Both molecules adopted beta-sheet conformations and showed similar hydrogen bonding patterns with one molecular surface forming two oxo hydrogen bonds and the other forming two thio hydrogen bonds. The crystal structure data for the two thioamides provided a validation of the thioamide parameters for the newly derived CFF91 force field because the observed crystal (phi, psi) angles were situated in the global minimum regions of the theoretical (phi, psi) map predicted using the parameters. In addition, the parameters were further validated because conformational energy minimization of the crystal structure produced low deviations in unit cell dimensions, bond lengths, bond angles and torsional angles, and a 120-ps molecular dynamics simulation also gave a low deviation for the most probable N-H...S=C bond distance.

Thionation of segetalins A and B, cyclic peptides with estrogen-like activity from seeds of Vaccaria segetalis

Thionation of estrogen-like active cyclic peptides, segetalins A (1) and B (2), with Lawesson's reagent provided each two thiosegetalins; thiosegetalin A1 [Gly-1-psi(CS-NH)-Val-2; Trp-5-psi (CS-NH)-Ala-6]segetalin A, thiosegetalin A2 [Gly-1-psi(CS-NH)-Val-2; Ala-6-psi(CS-NH)-Gly-1]segetalin A, thiosegetalin B1 [Gly-1-psi (CS-NH)-Val-2; Ala-3-psi(CS-NH)-Trp-4]segetalin B, and thiosegetalin B2 [Gly-1-psi(CS-NH)-Val-2; Trp-4-psi(CS-NH)-Ala-1]segetalin B. Thiosegetalin A2 only showed estrogen-like activity against ovariectomized rats. On the basis of their conformations analysed by NMR experiments, the backbone conformation was considered to play an important role in estrogen-like activity for segetalins.

Coupling constants and hydrogen bonds as experimental restraints in a distance geometry refinement protocol

A refinement procedure commonly used after distance geometry calculations has been modified to include the use of experimental restraints from coupling constants and hydrogen bonds. Fewer experimental distance constrains (NOEs) are available for peptides as compared to proteins; therefore it is important to incorporate other conformational restraints into refinement methods. The procedure was applied to a cyclic hexapeptide containing two thioamide substitutions, cyclo(-Gly1-Pro2-Phe3 psi [CS-NH]Val4-D-Phe5-Phe6 psi [CS-NH]-). Distance geometry was used to study this peptide, since no potential energy parameters, required in molecular mechanics or dynamics calculations, are available for the thioamide. This is a general problem in the study of peptidomimetics; physiochemical properties of heteroatoms are required within a self-consistent force field. Here, we illustrate the use of metric matrix distance geometry followed by refinement with distance and angle driven dynamics (DADD). We also introduce a new way to handle intramolecular hydrogen bonds by an additional very small and flexible restraint. This method is a viable alternative for the conformational examination of peptides and peptidomimetics. The modifications described here should also find use in the conformational determination of flexible regions of proteins, where the number of NOEs are limited.

Crystal and molecular structure of two geometrically restricted chemotactic tripeptides, analogues of formyl-methionine-leucine-phenylalanine

The crystal structures of HCO-Met-Leu-Phe-OC(CH3)3, (CH25H39N3O5S), fMLP-OtBu, and HCO-Met psi [CSNH]-Leu-Phe-OCH3, (C22H33N3O4S2), fMS LP-OMe, have been determined by single crystal X-ray diffraction, and their conformational properties investigated by molecular mechanics energy calculations. Crystals of fMLP-OtBu are monoclinic, space group P2(1), a = 12.027(4), b = 9.492(3), c = 12.660(4) A, beta = 101.99(3) degrees, Z = 2; those of fMS LP-OMe are orthorhombic, space group P2(1)2(1)2(1), a = 7.130(1), b = 12.097(2), c = 31.060(5) A, Z = 4. The first compounds fMLP-OtBu is the t-butyl ester of the tripeptide fMLP that represents one of the most potent compounds in inducing the lysozyme release from human neutrophils that reflects the chemotactic activity. From the crystal structure, it is shown that the orientation of the phenylalanine side chain is largely affected by the presence of the bulky group. fMSLP-OMe was shown to be inactive after thionation of the methionine residue in the original tripeptide. Nevertheless, the crystal structure does not reveal any influence of the presence of the thionated peptidic bond on the backbone conformation. The X-ray results have been used to generate parameters for empirical energy calculations. Subsequently, a strategy based on random generation of conformations followed by energy-minimization was applied to investigate the conformational space of thiopeptides, in comparison with normal peptides. From molecular free energy calculations, it is shown that the main influence of the introduction of a thioamide bond on the molecular structure is to prevent the existence of C7(eq) conformations involving the thiomethionine residue. Consequently, a larger number of conformers are found to form intramolecular hydrogen bonds involving the formyl group, reducing its availability to interact with the receptor. For the first time, the theoretical prediction of the existence of C7eq conformations for fMLP is made. The resulting conformers are compared to previously active structures of these chemotactic agents.

Intramolecular H-bonds and thioamide rotational isomerism in thiopeptides

Mono- and dithionated N-acyl amino acid and dipeptide N'-methylamides were synthesized using Lawesson's reagent and S-thioacetyl thioglycolic acid. The conformation of the thionated models was characterized by IR, 13C, and 1H NMR spectroscopy, including NOE experiments. The formation of -C = S...H-N-C = X (X = O or S) intramolecular H-bonds of the type 2----2, 1----3 and 1----4 was evidenced by the characteristic shifts of the IR stretching frequencies of the NH group. Act-Pro-NHCH3(4) and Act-Prot-NHCH3(5) were found to be present as mixtures of rotational isomers about the CS-N bond. 13C chemical shifts of the gamma- and beta-carbons of the proline ring elucidated the conformation (Z or E) of the tertiary thioamide group. Our results suggest that the conformation of thiopeptides is determined by two factors: 1) the H-bond donating and accepting ability of the thioamide group and 2) the repulsion between the thiocarbonyl sulfur atom and the side chain groups of the neighbouring amino acid residues.

Biological activities of cyclic enkephalin pseudopeptides containing thioamides as amide bond replacements

Analogs of H-Tyr-cyclo(N epsilon-D-Lys-Gly-Phe-Leu) have been prepared which contain thioamides at the 3-4 position (monothio), 3-4 and 5-2 positions (dithio), and 2-3, 3-4, and 5-2 positions (trithio). These compounds have been tested for opioid activity in mu- and delta-receptor selective bio- and binding assays. As the number of sulfurs increased, the biological activities dropped on the guinea pig ileum and fluctuated modestly on the mouse vas deferens assay. Surprisingly, the compounds displayed increasing delta selectivity as the number of sulfurs increased. In the binding assay, the thioamide analogs tended to retain affinity toward the mu receptor. The mono- and dithio-analogs were more mu selective than the parent, while the trithio-analog was more delta selective. These results suggest that the subtle exchange of sulfur for oxygen can have a significant impact on receptor selectivity and affinity, and probably reflect the different conformation/structural requirements for binding vs. the biological transduction event.

Structure of conformationally constrained peptides: from model compounds to bioactive peptides

The use of backbone conformational constraints has acquired increasing importance in the design and synthesis of structurally restricted agonists and antagonists of bioactive peptides. Here I discuss the preferred conformations of four among the most popular types of such peptide surrogates: (a) Peptides from C alpha, alpha-dialkylated residues, (b) tetrazolyl peptides, (c) (gamma- and delta-) lactam-containing peptides, and (d) thiated peptides. Emphasis is given to conformational energy computations and x-ray diffraction analyses of selected model compounds and analogues of small bioactive peptides such as the formylmethionyl tripeptide chemoattractant and MIF.

Stereochemistry of peptides containing a thioacyl group

Endothiopeptides are oligopeptides in which one or more oxoacyl moieties in peptide groups are replaced with thioacyl moieties. The stereochemical consequences of this replacement are discussed and compared with results from X-ray crystallographic determinations of small oligopeptides containing one or two thiopeptide groups. The analysis shows that the conformations normally observed around C alpha carbon atoms in proteins are also stereochemically favourable for peptides in which a thiopeptide group has been introduced. Limitations are only present in cases where the thiopeptide is part of structural elements like helices and beta-sheets. This opens the possibility of using one or more thiopeptide groups as functional modifiers of biologically active oligopeptide and protein molecules.

X-ray crystallography of peptides: the contributions of the Italian laboratories

The review article summarizes the most relevant solid state structural and conformational results obtained in the laboratories involved in Italy in the studies of synthetic and natural peptides by x-ray diffraction analyses. Some of the topics will include research studies carried out in other European countries, whereas in other cases studies carried out in Italy will be included in other review articles included in this volume. The review deals with peptides containing symmetrically achiral and unsymmetrically chiral C alpha,alpha-dialkylated glycine residues, peptides containing beta-alanine residues, alpha,beta-dehydroamino acid residues, and aminosuccinyl residues, peptides containing the thioamide surrogate, heterochiral peptides and several bioactive peptides systems with the proposed relationships between function and structure.