Amide Rotamers Research Articles

Relating Conformational Equilibria to Conformer-Specific Lipophilicities: New Opportunities in Drug Discovery.

Efficient drug discovery is based on a concerted effort in optimizing bioactivity and compound properties such as lipophilicity, and is guided by efficiency metrics that reflect both aspects. While conformation–activity relationships and ligand conformational control are known strategies to improve bioactivity, the use of conformer‐specific lipophilicities (logp) is much less explored. Here we show how conformer‐specific logp values can be obtained from knowledge of the macroscopic logP value, and of the equilibrium constants between the individual species in water and in octanol. This is illustrated with fluorinated amide rotamers, with integration of rotamer 19F NMR signals as a facile, direct method to obtain logp values. The difference between logp and logP optimization is highlighted, giving rise to a novel avenue for lipophilicity control in drug discovery.

Relating Conformational Equilibria to Conformer‐Specific Lipophilicities: New Opportunities in Drug Discovery

AbstractEfficient drug discovery is based on a concerted effort in optimizing bioactivity and compound properties such as lipophilicity, and is guided by efficiency metrics that reflect both aspects. While conformation–activity relationships and ligand conformational control are known strategies to improve bioactivity, the use of conformer‐specific lipophilicities (logp) is much less explored. Here we show how conformer‐specific logp values can be obtained from knowledge of the macroscopic logP value, and of the equilibrium constants between the individual species in water and in octanol. This is illustrated with fluorinated amide rotamers, with integration of rotamer 19F NMR signals as a facile, direct method to obtain logp values. The difference between logp and logP optimization is highlighted, giving rise to a novel avenue for lipophilicity control in drug discovery.

Diastereoselective Synthesis of (3R,5R)-γ-Hydroxypiperazic Acid

AbstractWe report an asymmetric synthesis of the (3R,5R)-γ-hydroxypiperazic acid (γ-OHPiz) residue encountered in several bioactive nonribosomal peptides. Our strategy relies on a diastereoselective enolate hydroxylation reaction and electrophilic N-amination to provide the acyclic γ-OHPiz precursor. This orthogonally protected α-hydrazino acid intermediate is amenable to late-stage diazinane ring formation following incorporation into a peptide chain. We determined the N-terminal amide rotamer propensity of the γ-OHPiz residue and showed that the γ-OH substituent enhances trans-amide bias relative to piperazic acid.

δ-Azaproline and Its Oxidized Variants.

Peptides featuring backbone N-amino substituents exhibit unique conformational properties owing to additional electrostatic, hydrogen-bonding, and steric interactions. Here, we describe the synthesis and conformational analysis of three δ-azaproline derivatives as potential proline surrogates. Our studies demonstrate stereoelectronic tuning of heterocyclic ring pucker, cis/trans amide propensity, and amide isomerization barriers within a series of oxidation state variants. A combination of NMR, X-ray diffraction, and density functional theory calculations shows that electron density and hybridization at the δ position play a dominant role in the conformational preferences of each analogue. Both δ-azaproline and γ,δ-dehydro-δ-azaproline exhibit strong trans amide rotamer propensities irrespective of ring conformation, while a novel residue, γ-oxo-δ-azaproline, features rapid amide isomerization kinetics and isoenergetic amide bond geometries influenced by torsional strain and H-bonding interactions. The introduction of the δ heteroatom in each residue allows the decoupling of structural effects that are typically linked in proline and its pyrrolidine-substituted analogues. δ-Azaproline derivatives thus represent useful probes of prolyl amide isomerism with potential applications in peptidomimetic drug design and protein folding.

Synthesis of Enantiopure ε-Oxapipecolic Acid.

A six-step synthesis of orthogonally protected (S)-ε-oxapipecolic acid is described, starting from a commercially available glutamate diester. The approach features mCPBA-mediated amine oxidation and an intramolecular Mitsunobu reaction to form the tetrahydrooxazine ring. The enantiopure building block was employed in the synthesis of a short model peptide to determine the amide rotamer preference N-terminal to the cyclic residue. In contrast to pipecolic acid, which exhibits a high cis amide population, the ε heteroatom in oxapipecolic acid exerts a strong trans substantiating effect through lone pair repulsion.

Deconvolution of E/Z tetrahydroisoquinoline amide rotamers and conformers from a marine-derived Streptomyces strain

A collaborative program to discover new specialized metabolites from aquatic environments of Iceland led to the deconvolution of tetrahydroisoquinoline amide E/Z rotamers [(E/Z)-N-acetyl-MY336-a; 1] and conformers produced by a Streptomyces sp. All structures were elucidated by NMR and MS analysis, and interpretation of electronic circular dichroism (ECD) data. ECD and optical rotation (OR) simulations permitted the unequivocal assignment of the absolute configuration of compound 1 and provided an important example of delineating the spectroscopic contributions of equilibrating rotamers and boat/chair conformers of a common natural product scaffold.

Conformational Control of Chiral Amido-Thiourea Catalysts Enables Improved Activity and Enantioselectivity.

While aryl pyrrolidinoamido-thioureas derived from α-amino acids are effective catalysts in a number of asymmetric transformations, they exist as mixtures of slowly interconverting amide rotamers. Herein, the compromising role of amide bond isomerism is analyzed experimentally and computationally. A modified catalyst structure that exists almost exclusively as a single amide rotamer is introduced. This modification is shown to result in improved reactivity and enantioselectivity by minimizing competing reaction pathways.

Crystal structures of three 3,4,5-tri-meth-oxy-benzamide-based derivatives.

The crystal structures of three benzamide derivatives, viz. N-(6-hy-droxy-hex-yl)-3,4,5-tri-meth-oxy-benzamide, C16H25NO5, (1), N-(6-anilinohex-yl)-3,4,5-tri-meth-oxy-benzamide, C22H30N2O4, (2), and N-(6,6-di-eth-oxy-hex-yl)-3,4,5-tri-meth-oxy-benzamide, C20H33NO6, (3), are described. These compounds differ only in the substituent at the end of the hexyl chain and the nature of these substituents determines the differences in hydrogen bonding between the mol-ecules. In each mol-ecule, the m-meth-oxy substituents are virtually coplanar with the benzyl ring, while the p-meth-oxy substituent is almost perpendicular. The carbonyl O atom of the amide rotamer is trans related with the amidic H atom. In each structure, the benzamide N-H donor group and O acceptor atoms link the mol-ecules into C(4) chains. In 1, a terminal -OH group links the mol-ecules into a C(3) chain and the combined effect of the C(4) and C(3) chains is a ribbon made up of screw related R 2 (2)(17) rings in which the ⋯O-H⋯ chain lies in the centre of the ribbon and the tri-meth-oxy-benzyl groups forms the edges. In 2, the combination of the benzamide C(4) chain and the hydrogen bond formed by the terminal N-H group to an O atom of the 4-meth-oxy group link the mol-ecules into a chain of R 2 (2)(17) rings. In 3, the mol-ecules are linked only by C(4) chains.

Synthesis, Characterization, and Conformational Study of Acylhydrazones of α,β‐Unsaturated Aldehydes

ABSTRACTNew acylhydrazone derivatives 1–6 have been synthesized by condensation of tert‐butylphenoxyhydrazide and cinnamaldehyde A or β‐chloro‐α,β‐unsaturated aldehydes B–F. They were characterized by IR, (1H, 13C, 19F) nuclear magnetic resonance (NMR), and high‐resolution mass spectroscopy. The NMR data show the existence of the cis/trans‐amide conformers due to N–C(O) bond rotation in addition to the E/Z isomers around the C=C bond of some of the starting aldehydes. The solvent polarity effects on the ratios of the cis/trans‐amide rotamers have also been investigated. Importantly, rotational barriers around the N–C(O) bond for all compounds 1–6 (62.9–68.8 kJ mol–1) were calculated using the coalescence‐temperature method according to the Eyring equation. The results are discussed and compared with those previously reported for related acylhydrazones of aryl adehydes and acetone.

Energetic contribution to both acidity and conformational stability in peptide models

The acidity difference of the amide rotamers has been revised for a large set ofN-acetyl amino acids.

Efficient Synthesis of Conformationally Restricted Apoptosis Inhibitors Bearing a Triazole Moiety.

Apoptosis is a biological process relevant to different human diseases that is regulated through protein-protein interactions and complex formation. Peptidomimetic compounds based on linear peptoids and cyclic analogues with different ring sizes have been previously reported as potent apoptotic inhibitors. Among them, the presence of cis/trans conformers of an exocyclic tertiary amide bond in slow exchange has been characterized. This information encouraged us to perform an isosteric replacement of the amide bond by a 1,2,3-triazole moiety, in which different substitution patterns would mimic different amide rotamers. The syntheses of these restricted analogues have been carried out through an Ugi multicomponent reaction followed by an intramolecular cyclization. The unexpected formation of a β-lactam scaffold prompted us to study the course of the intramolecular cyclization of the Ugi adducts. In order to modulate this cyclization, a small library of compounds bearing both heterocyclic scaffolds has been synthesized and their activities as apoptosis inhibitors have been evaluated.

Unique Structural Properties of 2,4,6-Tri-tert-butylanilide: Isomerization and Switching between Separable Amide Rotamers through the Reaction of Anilide Enolates

Herein, we report a unique structural property of 2,4,6-tri-tert-butylanilide, which can be separated into its amide rotamers at room temperature. Interconversion between the rotamers of anilide enolates occurs readily at room temperature and their reaction with electrophiles gives mixtures of the rotamers in a ratio that depends on the reactivity of the corresponding electrophile. That is, the reaction of the 2,4,6-tri-tert-butylacetanilide enolate with reactive electrophiles, such as allyl bromide or protic acids, gives mixtures of the anilide rotamers in which the E rotamer is the major component, whereas less-reactive electrophiles, such as 1-bromopropane and 2-iodopropane, yield mixtures of the rotamers in which the Z rotamer is the major component. The rotameric ratio of the product is also strongly dependent on the reactivity of the anilide enolate. Switching between the anilide rotamers can be achieved through protonation of a less-reactive enolate by a less-reactive protic acid and thermal isomerization of the anilide.

Optimizing the control of apoptosis by amide/triazole isosteric substitution in a constrained peptoid

Apoptosis is a biological process relevant to several human diseases that is strongly regulated through protein–protein complex formation. We have previously reported a peptidomimetic compound as potent apoptotic modulator. Structural studies of this compound showed the presence of cis/trans isomers of the exocyclic tertiary amide bond in slow exchange. This information encouraged us to perform an isosteric replacement of the amide bond by a 1,2,3-triazole moiety, where different substitution patterns would mimic different amide rotamers. The syntheses of these restricted analogs have been carried out using the Ugi multicomponent reaction followed by an intramolecular cyclization. Unexpectedly, for one of the proposed structures, a novel β -lactam compound was formed. All compounds showed to efficiently inhibit apoptosis, in vitro and in cellular extracts, with slight differences for the corresponding regioisomers. We propose the binding to Apaf-1 as the inhibition mechanism.

Design and conformational analysis of peptoids containing N-hydroxy amides reveals a unique sheet-like secondary structure.

N-hydroxy amides can be found in many naturally occurring and synthetic compounds and are known to act as both strong proton donors and chelators of metal cations. We have initiated studies of peptoids, or N-substituted glycines which contain N-hydroxy amide side chains to investigate the potential effects of these functional groups on peptoid backbone amide rotamer equilibria and local conformations. We reasoned that the propensity of these functional groups to participate in hydrogen bonding could be exploited to enforce intramolecular or intermolecular interactions that yield new peptoid structures. Here, we report the design, synthesis, and detailed conformational analysis of a series of model N-hydroxy peptoids. These peptoids were readily synthesized, and their structures were analyzed in solution by 1D and 2D NMR and in the solid-state by X-ray crystallography. The N-hydroxy amides were found to strongly favor trans conformations with respect to the peptoid backbone in chloroform. More notably, unique sheet-like structures held together via intermolecular hydrogen bonds were observed in the X-ray crystal structures of an N-hydroxy amide peptoid dimer, which to our knowledge represent the first structure of this type reported for peptoids. These results suggest that the N-hydroxy amide can be utilized to control both local backbone geometries and longer-range intermolecular interactions in peptoids, and represents a new functional group in the peptoid design toolbox.

Fructose‐Based Proline Analogues: Exploring the Prolyl trans/cis‐Amide Rotamer Population in Model Peptides

AbstractA D‐fructose moiety in which a D‐proline ring has been engineered with a spiranic junction in the glycidic scaffold has been used as a proline mimetic. The bicyclic structure, which possesses high structural rigidity, was then included in model peptides to explore their prolyl cis/trans amide rotamer populations. Model peptide conformations were studied by molecular dynamics and NMR experiments.

Diverging Chemoselective Reactions of Separable Amide Rotational Isomers

Diverging chemoselective reactions of a pair of amide rotamers have been observed by separating the rotamers and then reacting them individually. Reduction of (Z)-N-allyl-2-(phenylselanyl)-N-(2,4,6-tri-tert-butylphenyl)acetamide with tributyltin hydride at room temperature provides only the product of 5-exo cyclization, 4-methyl-1-(2,4,6-tri-tert-butylphenyl)pyrrolidin-2-one. In contrast, reduction of the corresponding (E) amide rotational isomer under identical conditions provides only the reduced product, (E)-N-allyl-N-(2,4,6-tri-tert-butylphenyl)acetamide. Such diverging reactions of rotamers may be common in transformations involving reactive intermediates (carbenes, radicals, organometallic intermediates) that have low barriers to onward reactions relative to amide rotation.

Highly Selective Stereodivergent Synthesis of Separable Amide Rotamers, by Using Pd Chemistry, and Their Thermodynamic Behavior

By using Pd chemistry, a highly selective stereodivergent synthesis of separable amide rotamers was achieved. Allylation of 2,4,6-tri-tert-butylanilides using a pi-allyl-Pd catalyst gave N-allylated anilides with moderate-to-excellent Z-rotamer selectivity (Z/E = 3 to > 50). The Z-rotamer selectivity depends considerably on the substituent on the anilide substrates. On the other hand, the E rotamers of N-allylated 2,4,6-tri-tert-butylanilides were obtained with almost complete selectivity (E/Z > 50) through O-allylation of 2,4,6-tri-tert-butylanilides and the subsequent Pd(II)-catalyzed Claisen rearrangement of the resulting O-allyl imidate. The prepared anilide rotamers changed to equilibrium mixtures in which the E rotamer was the major isomer when heated in toluene.

Stereoselective synthesis of separable amide rotamers using π-allyl-Pd catalyst and their thermodynamic behavior

Separable amide rotamers were prepared with moderate to excellent Z-selectivities by N-allylation of 2,4,6-tri- tert-butyl-NH-anilides using a π-allyl-Pd catalyst. The present allylation proceeded through a unique mechanism involving O-allylation and the subsequent O, N-allylic rearrangement. The prepared amide rotamers of Z-major changed to equilibrium mixtures of E-major when heated in toluene.

How Do Analogous α-Chloroenamides and α-Iodoenamides Give Different Product Distributions in 5-EndoRadical Cyclizations?

5-Endo cyclizations of N-alkenyl carbamoylmethyl radicals provide gamma-lactam radicals, which in turn evolve to reduced or non-reduced (alkene) products depending on reagents and reaction conditions. Several groups have made surprising observations that chlorides are better radical precursors than iodides in such cyclizations. Here is described a detailed study of tin and silicon hydride-mediated radical cyclizations of N-benzyl-2-halo-N-cyclohex-1-enylacetamides. The ratios of directly reduced, cyclized/reduced, and cyclized/non-reduced products depend not only on the reaction conditions and reducing reagent but also on the precursor. Prior explanations for the precursor-dependent product ratios based on amide rotamer effects are ruled out. The precursor-dependent behavior is further dissected into two different effects: (1) the ratio of cyclized/reduced products to cyclized/non-reduced products depends on the ability of the radical precursor to react with the product gamma-lactam radical in competition with tin hydride (iodides can compete, chlorides cannot), and (2) the occurrence of large amounts of directly reduced (noncyclized) products in the case of iodides is attributed to a competing ionic chain reaction by which the precursor is reductively deiodinated with HI. This side reaction is not available to chlorides, thereby explaining why the chlorides are better precursors in such reactions. The ability of the iodides to provide cyclized products can be largely restored by adding base. The chlorides and iodides then become complementary precursors, with chlorides giving largely cyclized/reduced products and iodides giving largely cyclized/non-reduced products.

Self-Consistent Assignment of Asparagine and Glutamine Amide Rotamers in Protein Crystal Structures

The current protein structure database contains unfavorable Asn/Gln amide rotamers in the order of 20%. Here, we derive a set of self-consistent potential functions to identify and correct unfavorable rotamers. Potentials of mean force for all heavy atoms are compiled from a database of high-resolution protein crystal structures. Starting from erroneous data, a refinement-correction cycle quickly converges to a self-consistent set of potentials. The refinement is entirely driven by the deposited structure data and does not involve any assumptions on molecular interactions or any artificial constraints. The refined potentials obtained in this way identify unfavorable rotamers with high confidence. Since the state of Asn/Gln rotamers is largely determined by hydrogen bond interactions, the features of the respective potentials are of interest in terms of molecular interactions, protein structure refinement, and prediction. The Asn/Gln rotamer assignment is available as a public web service intended to support protein structure refinement and modeling.