Stereochemistry of peptides containing a thioacyl group

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.

Desolvation of Peptide Bond by O to S Substitution Impacts Protein Stability

Amino acid side chains are key to fine-tuning the microenvironment polarity in proteins composed of polar amide bonds. Here, we report that substituting an oxygen atom of the backbone amide bond with sulfur atom desolvates the thioamide bond, thereby increasing its lipophilicity. The impact of such local desolvation by O to S substitution in proteins was tested by synthesizing thioamidated variants of Pin1 WW domain. We observe that a thioamide acts in synergy with nonpolar amino acid side chains to reduce the microenvironment polarity and increase protein stability by more than 14 °C. Through favorable van der Waals and hydrogen bonding interactions, this single atom substitution significantly stabilizes proteins without altering the amino acid sequence and structure of the native protein.

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.

Asymmetric Catalysis Mediated by Synthetic Peptides, Version 2.0: Expansion of Scope and Mechanisms

Low molecular weight synthetic peptides have been demonstrated to be effective catalysts for an increasingly wide array of asymmetric transformations. In many cases, these peptide-based catalysts have enabled novel multifunctional substrate activation modes and unprecedented selectivity manifolds. These features, along with their ease of preparation, modular and tunable structures, and often biomimetic attributes make peptides well-suited as chiral catalysts and of broad interest. Many examples of peptide-catalyzed asymmetric reactions have appeared in the literature since the last survey of this broad field in Chemical Reviews (Chem. Rev. 2007, 107, 5759-5812). The overarching goal of this new Review is to provide a comprehensive account of the numerous advances in the field. As a corollary to this goal, we survey the many different types of catalytic reactions, ranging from acylation to C-C bond formation, in which peptides have been successfully employed. In so doing, we devote significant discussion to the structural and mechanistic aspects of these reactions that are perhaps specific to peptide-based catalysts and their interactions with substrates and/or reagents.

Effects of isosteric substitutions on the conformational preference and cis–trans isomerization of proline-containing peptides

Isosteric substitutions of the peptide CO group by CS and CSe groups increased thetranspopulation and rotational barrier to the prolylcis–transisomerization of proline-containing peptides.

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.

Mapping backbone and side-chain interactions in the transition state of a coupled protein folding and binding reaction

Understanding the mechanism of protein folding requires a detailed knowledge of the structural properties of the barriers separating unfolded from native conformations. The S-peptide from ribonuclease S forms its α-helical structure only upon binding to the folded S-protein. We characterized the transition state for this binding-induced folding reaction at high resolution by determining the effect of site-specific backbone thioxylation and side-chain modifications on the kinetics and thermodynamics of the reaction, which allows us to monitor formation of backbone hydrogen bonds and side-chain interactions in the transition state. The experiments reveal that α-helical structure in the S-peptide is absent in the transition state of binding. Recognition between the unfolded S-peptide and the S-protein is mediated by loosely packed hydrophobic side-chain interactions in two well defined regions on the S-peptide. Close packing and helix formation occurs rapidly after binding. Introducing hydrophobic residues at positions outside the recognition region can drastically slow down association.

Conformational analysis of thiopeptides: free energy calculations on the effects of thio-substitutions on the conformational distributions of alanine dipeptides

When the oxygen atom in a peptide bond is replaced by a sulfur atom, the restriction in the available conformational space and the ability of thioamides to confer resistance to enzymatic degradation renders thioamides as potentially useful building blocks for drug design and protein engineering. The solvation free energy differences between conformers of the same dipeptide can be high. Yet, previous conformational studies, basing on the (phi, psi) conformational energy maps of thio-substituted dipeptides, neglected both explicit water interactions and free energy considerations. In this paper, the (phi, psi) conformational free energy maps are obtained by single umbrella sampling in an explicit water environment for both alanine dipeptide and the corresponding thioamide derivatives. The phi and psi angles for the minima in the relative energy maps calculated with dielectric of 80 are similar to the corresponding phi and psi angles in the relative free energy maps for both Ac-Ala-NHMe (Ac: acetyl; Ala: alanine) and Act-Alat-NHMe (Act: thio-acetyl; Alat: thio-alanine). However, some large differences between the relative energy and relative free energy of major minima indicate that the consideration of free energy is important in determination of the relative occupancy of particular minima. Free energy maps for both Ac-Ala-NHMe and Act-Alat-NHMe show that thio-substitution favors conformations where phi < 0 because of the deeper beta and alphaR minima. The changes in the position and relative stability of minima were explained in terms of the destabilization of the regions near phi = -120, 0 and 120, psi = 60, -60, 180, which correspond to the increased steric hindrance due to the bulkier sulfur atom.

Synthesis and PKC isozyme surrogate binding of indothiolactam-V, a new thioamide analogue of tumor promoting indolactam-V

To investigate the role of the amide group of (-)-indolactam-V (1) on PKC binding, we synthesized (-)-indothiolactam-V (2), a new thioamide analogue of 1, by microbial conversion using Streptomyces blastmyceticum. Compounds 2 and 1 showed similar binding affinities to conventional PKCs but 2 had lower affinities to novel PKCs, suggesting that novel PKCs recognize amide modifications more effectively than conventional PKCs.

Endothiopeptide inhibitors of HIV-1 protease

Endothiopeptide inhibitors of HIV-1 protease were synthesized by chemical and enzymatic methods to individually replace each backbone amide bond in 1 with a thioamide-linkage. Interestingly, agent 7, which contains a thioamide-linkage between the P2' and P3' positions of 1, was the most potent, competitive inhibitor of HIV-1 protease with a Ki of 3.4 microM.

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.

Unusual thionation of a cyclic hexapeptide. Conformational changes and dynamics

One carbonyl oxygen of the cyclic hexapeptide cyclo(-Gly1-Pro2-Phe3-Val4-Phe5-Phe6-) (A) can be selectively exchanged with sulphur using Yokoyama's reagent. Surprisingly it was not the C=] of Gly1 but that of Phe5 which was substituted and cyclo(-Gly1-Pro2-Phe3-Val4-Phe5 psi [CS-NH]Phe6-) (B) was obtained. Thionation results in a conformational change of the peptide backbone although the C=O of Phe5 and the corresponding C=S are not involved in internal hydrogen bonds. Two isomers in slow exchange, containing a cis Gly1-Pro2 bond in a beta VIa-turn (minor) and a trans Gly-Pro bond in a beta II'-turn (major), were analyzed by restrained molecular dynamics in vacuo and in DMSO as well as using time dependent distance constraints. It is impossible to fit all experimental data to a static structure of each isomer. Interpreting the conflicting NOEs, local segment flexibility is found. MD simulations lead to a dynamic model for each structure with evidence of an equilibrium between a beta I- and beta II-turn about the Val4-Phe5 amide bond in both the cis and trans isomers. Additionally proton relaxation rates in the rotating frame (R1 rho) were measured to verify the assumption of this fast beta I/beta II equilibrium within each isomer. Significant contributions to R1 rho-rates from intramolecular motions were found for both isomers. Therefore it is possible to distinguish between at least four conformers interconverting on different time scales based on NMR data and MD refinement. This work shows that thionation is a useful modification of peptides for conformation-activity investigations.

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.

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.

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.