Isomeric Amides Research Articles

Thermoswitching of Helical Inversion of Dynamic Polyphenylacetylenes through cis-trans Isomerization of Amide Pendants

The cis-trans isomerization of amides plays a vital role in all kinds of structural changes and biological activities, involving protein folding, protein misfolding, and even protein molecular recognition. However, the helical inversion of synthetic macromolecules arising from the cis-trans isomerization of tertiary amides, as a good mimic of natural protein, has been rarely researched. Herein, we synthesized meta-disubstituted polyphenylacetylenes (PPAs) with different N-substituted tertiary amides as one of the pendants, poly{(−)-3-methoxycarbonyl-5-[N-methyl-N-(S)-(1-phenylethyl)carbamoyl]phenylacetylene}(sP-NMe) and poly{(−)-3-methoxycarbonyl-5-[N-propyl -N-(S)-(1-phenylethyl)carbamoyl]phenylacetylene} (sP-NPr). The cis-trans isomerization of amides was investigated by a combinational analysis of 1H/13C nuclear magnetic resonance (NMR), heteronuclear multiple quantum coherence (HMQC), variable-temperature NMR, Raman spectroscopy, ultraviolet–visible (UV–vis) spectroscopy, electronic circular dichroism (ECD), vibrational circular dichroism (VCD), and computer calculations. The substituted amide of sP-NMe favors the trans isomer at low temperatures, and the polyene main chain takes the right-handed helical conformation. When increasing the temperature, the ratio of the cis isomer in sP-NMe increases, which causes helical inversion. The screw sense of the polymer backbone of sP-NMe can be thermoreversibly switched upon tuning the cis-trans isomerization equilibrium of the tertiary amide pendant. In comparison, sP-NPr has the left-handed conformation with the majority of the cis isomer owing to the bulky propyl group, and cis-trans isomerization cannot induce helical inversion upon thermal treatment. The results reveal that helical inversion caused by the cis-trans isomerization of amide groups is highly dependent on the size of N-alkyl substituents.

Structural Flexibility of Cyclosporine A Is Mediated by Amide Cis-Trans Isomerization and the Chameleonic Roles of Calcium.

Falling outside of Lipinski's rule of five, macrocyclic drugs have accessed unique binding sites of their target receptors unreachable by traditional small molecules. Cyclosporin(e) A (CycA), an extensively studied macrocyclic natural product, is an immunosuppressant with undesirable side effects such as electrolytic imbalances. In this work, a comprehensive view on the conformational landscape of CycA, its interactions with Ca2+, and host-guest interactions with cyclophilin A (CypA) is reported through exhaustive analyses that combine ion-mobility spectrometry-mass spectrometry (IMS-MS), nuclear magnetic resonance (NMR) spectroscopy, distance-geometry modeling, and NMR-driven molecular dynamics. Our IMS-MS data show that CycA can adopt extremely compact conformations with significantly smaller collisional cross sections than the closed conformation observed in CDCl3. To adopt these conformations, the macrocyclic ring has to twist and bend via cis-trans isomerization of backbone amides, and thus, we termed this family of structures the "bent" conformation. Furthermore, NMR measurements indicate that the closed conformation exists at 19% in CD3OD/H2O and 55% in CD3CN. However, upon interacting with Ca2+, in addition to the bent and previously reported closed conformations of free CycA, the CycA:Ca2+ complex is open and has all-trans peptide bonds. Previous NMR studies using calcium perchlorate reported only the closed conformation of CycA (which contains one cis peptide bond). Here, calcium chloride, a more biologically relevant salt, was used, and interestingly, it helps converting the cis-MeLeu9-MeLeu10 peptide bond into a trans bond. Last, we were able to capture the native binding of CycA and CypA to give forth evidence that IMS-MS is able to probe the solution-phase structures of the complexes and that the Ca2+:CycA complex may play an essential role in the binding of CycA to CypA.

Formation of phosphine imide (HNPH3) and its phosphinous amide (H2N–PH2) isomer

We present the first formation of the previously elusive phosphine imide (HN[double bond, length as m-dash]PH3) along with its phosphinous amide (H2N-PH2) isomer via exposure of phosphine (PH3) and ammonia (NH3) ices to ionizing radiation. Our approach may be extended to prepare, separate, and detect highly reactive compounds such as intermediates of Wittig reactions.

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.

Синтез имидов на основе фенилциклоалкандикарбоновых кислот и производных трифторметиланилина

Previously it was shown that the stereochemical result of the alkylation reaction of benzene with cycloalkanedicarboxylic acids depends on the order of mixing the reagents. Based on this, we have developed methods for the synthesis of phenylcycloalkanedicarboxylic acids and methods for the separation of their isomers. The resulting diastereomerically pure compounds were used to synthesize new imides containing the trifluoromethyl group, which are potentially biologically active substances with antitumor properties. Since aromatic amines containing the CF3 group are weak nucleophiles, during the reaction both complete and incomplete closure of the imide cycle can be observed. The research problem was to study the dependence of the character of the reaction products and their ratio (imide/amides) on the flow conditions: the solvent used and the use of auxiliary reagents. When carrying out the imidization reaction in acetic acid, the formation of a mixture of imide and isomeric amides is observed, and the use of tea in toluene or DMF and in the system of acetic acid – pyridine, taken in a 2 : 3 ratio, leads to the formation of an imide only, but with different yields. Were tested methods for obtaining imides in pyridine through the stage of obtaining dichlorohydrin, which were obtained using thionyl chloride and using triphenylphosphine – carbon tetrachloride. Imides were also obtained in good yields in one-pot reactions by heating a mixture of pyridine, acid, amine, and thionyl chloride. The structure of the new compounds was confirmed by IR spectroscopy, 1H, 13C NMR spectra, capillary electrophoresis, elemental analysis and HPLC.

Amide nitrogen pyramidalization changes lactam amide spinning

Although cis-trans lactam amide rotation is fundamentally important, it has been little studied, except for a report on peptide-based lactams. Here, we find a consistent relationship between the lactam amide cis/trans ratios and the rotation rates between the trans and cis lactam amides upon the lactam chain length of the stapling side-chain of two 7-azabicyclo[2.2.1]heptane bicyclic units, linked through a non-planar amide bond. That is, as the chain length increased, the rotational rate of trans to cis lactam amide was decreased, and consequently the trans ratio was increased. This chain length-dependency of the lactam amide isomerization and our simulation studies support the idea that the present lactam amides can spin through 360 degrees as in open-chain amides, due to the occurrence of nitrogen pyramidalization. The tilting direction of the pyramidal amide nitrogen atom of the bicyclic systems is synchronized with the direction of the semicircle-rotation of the amide.

Spectroscopic Characterization of an Extensive Set of c-Type Peptide Fragment Ions Formed by Electron Transfer Dissociation Suggests Exclusive Formation of Amide Isomers.

Electron attachment dissociation (electron capture dissociation (ECD) and electron transfer dissociation (ETD)) applied to gaseous multiply protonated peptides leads predominantly to backbone N–Cα bond cleavages and the formation of c- and z-type fragment ions. The mechanisms involved in the formation of these ions have been the subject of much discussion. Here, we determine the molecular structures of an extensive set of c-type ions produced by ETD using infrared ion spectroscopy. Nine c3- and c4-ions are investigated to establish their C-terminal structure as either enol-imine or amide isomers by comparison of the experimental infrared spectra with quantum-chemically predicted spectra for both structural variants. The spectra suggest that all c-ions investigated possess an amide structure; the absence of the NH bending mode at approximately 1000–1200 cm–1 serves as an important diagnostic feature.

Rhodium-Catalyzed Domino Hydroformylation/Double-Cyclization Reaction of Arylacetylenecarboxamides: Diastereoselectivity Studies and Application in the Synthesis of 1-Azabicyclo[x.y.0]alkanes.

A domino method for the rapid syntheses of 1-azabicyclo[x.y.0]alkane scaffolds, such as indolizidines, quinolizidines, decahydropyridoazepines, and their derivatives, has been developed. This strategy involved a rhodium-catalyzed hydroformylation of allyl-, 3-butenyl-, or homoallyl amides, followed by two spontaneous ring closures under mild conditions. The reaction scope and diastereoselectivity were fully explored by changing the substitution pattern on the amide and by altering the length of the carbon chain. This method was applied to the syntheses of natural alkaloids tashiromine and epilupinine. The clear differences between the reactivities of two isomeric amide substrates, 3-butenamide 1 j and homoallyl amide 1 i, could be attributed to better HOMO-LUMO overlap in the transition states that were derived from butenamides during cyclization. This explanation was supported by DFT calculations.

Density Functional Studies on Secondary Amides: Role of Steric Factors in Cis/Trans Isomerization.

Cis/trans isomerization of amide bonds is a key step in a wide range of biological and synthetic processes. Occurring through C-N amide bond rotation, it also coincides with the activation of amides in enzymatic hydrolysis. In recently described QM studies of cis/trans isomerization in secondary amides using density functional methods, we highlighted that a peptidic prototype, such as glycylglycine methyl ester, can suitably represent the isomerization and complexities arising out of a larger molecular backbone, and can serve as the primary scaffold for model structures with different substitution patterns in order to assess and compare the steric effect of the substitution patterns. Here, we describe our theoretical assessment of such steric effects using tert-butyl as a representative bulky substitution. We analyze the geometries and relative stabilities of both trans and cis isomers, and effects on the cis/trans isomerization barrier. We also use the additivity principle to calculate absolute steric effects with a gradual increase in bulk. The study establishes that bulky substitutions significantly destabilize cis isomers and also increases the isomerization barrier, thereby synergistically hindering the cis/trans isomerization of secondary amides. These results provide a basis for the rationalization of kinetic and thermodynamic properties of peptides with potential applications in synthetic and medicinal chemistry.

Solvatochromism, thermochromism and density functional theory studies of Copper(II) complexes containing hemilabile tetradentate ligand

Two complexes of [Cu(L)H2O](ClO4)2,1 and [Cu(L)H2O](NO3)2, 2 containing hemilabile tetradentate ligand of 3,3'-(piperazine-1,4-diyl)dipropanamide, L, were synthesized and characterized by elemental analyses, spectroscopic (IR, UV–Vis, X-ray) data, molar conductance measurements and X-ray crystallography. The solvatochromic behavior of complex 1 was examined in the selected solvents (nitromethane, acetonitrile, propionitrile, acetone, tetrahydrofuran, ethanol, methanol, dimethylformamide, dimethylsulfoxide, and hexamethylphosphorictriamide), observing positive solvatochromism. The observed solvatochromism was analyzed by a statistical method. The obtained results confirm that the donor number (DN) parameter has the dominant contribution in the observed solvatochromism. For cationic complex 2 density functional theory (DFT) and time-dependent density functional theory (TD-DFT) calculations was carried out to explore the mechanism of the solvatochromic behavior of the complex and satisfactory theoretical–experimental agreement was achieved. Additional information about the relative stability of CuN(amide) over CuO(amide) isomers was obtained by DFT analysis. The complexes were also observed to exhibit thermochromism in the solvent of dimethyl sulfoxide.

Analytical studies on the 2-naphthoyl substituted-1-n-pentylindoles: Regioisomeric synthetic cannabinoids

The six 1-n-pentyl-2-, 3-, 4-, 5-, 6- and 7-(2-naphthoyl)-indoles each have the same substituents attached to the indole ring, identical elemental composition (C24H23NO) yielding identical nominal and accurate masses. The electron ionization mass spectra of the 2-naphthoyl substituted isomers share equivalent major fragment ions resulting from cleavage of the groups attached to the central indole nucleus with some differences in relative abundances.These six regioisomers were successfully resolved on an Rtx-5 and Rxi-17Sil MS stationary phases and the molecules having both substituent groups on the same side of the indole ring (1,2- and 1,7-substituents) show the least retention. The more linear molecules have higher relative retention properties. A comparison of the GC properties of the 1-naphthoyl- and 2-naphthoyl groups attached at identical positions of the indole ring showed higher GC retention for the 2-naphthoyl substituted isomer in all cases evaluated.The amide inverse isomers (1-naphthoyl-3-n-pentylindoles) were separated from the 1-n-pentyl-3-naphthoyl-indoles on an Rtx-200 stationary phase. The two inverse amide isomers having the 1- and 2-naphthoyl groups substituted at the 1-position of the indole ring elute before either of the N-alkyl-indole isomers having the 1- and 2-naphthoyl groups substituted at the 3-position of the indole ring. The amide inverse isomers yield EI mass spectra easily distinguishing these amides from the ketone isomers having the naphthoyl groups at the indole 3-position.

Selective opioid growth factor receptor antagonists based on a stilbene isostere

As part of an ongoing drug development effort aimed at selective opioid receptor ligands based on the pawhuskin natural products we have synthesized a small set of amide isosteres. These amides were centered on lead compounds which are selective antagonists for the delta and kappa opioid receptors. The amide isomers revealed here show dramatically different activity from the parent stilbene compounds. Three of the isomers synthesized showed antagonist activity for the opioid growth factor (OGF)/opioid growth factor receptor (OGFR) axis which is involved in cellular and organ growth control. This cellular signaling mechanism is targeted by “low-dose” naltrexone therapy which is being tested clinically for multiple sclerosis, Crohn’s disease, cancer, and wound healing disorders. The compounds described here are the first selective small molecule ligands for the OGF/OGFR system and will serve as important leads and probes for further study.

Peptidyl-Prolyl Model Study: How Does the Electronic Effect Influence the Amide Bond Conformation?

The triple-helical structure of collagen, the most abundant protein in animal bodies, owes its stability to post-translationally installed hydroxyl groups at position 4 of prolyl residues. To shed light on the nature of this phenomenon, we have examined the influence of the 4-substituent on the amide isomerism in peptidyl-prolyl analogues. The rigid bicyclic skeleton of 2,4-methanoprolines allowed us to follow the through-bond impact of the substituent group (electronic effect) without the side-chain conformation being affected by a stereoelectronic effect. These proline analogues were prepared by [2 + 2] photocycloaddition of (2-allylamino)acrylic acid derivatives. Subsequent pKa studies demonstrated a remarkable electronic effect of the 4-fluorine substitution, while the effect of the 4-methyl group was negligible. The trans/cis amide ratio was measured in model compounds under low temperature conditions. The observed prevalence for a trans-amide is extraordinary, and in this regard, 2,4-methanoproline is closer to primary α-amino acids than to proline. At the same time the amide rotation velocities were 3-4 orders of magnitude higher when compared to N-acetylprolyl. Finally, our results indicate that the electronic effect of the 4-substituent only affects the kinetics of the amide isomerization but not the thermodynamic prevalence for the trans-rotamer.

Isomerization of N-Allyl Amides To Form Geometrically Defined Di-, Tri-, and Tetrasubstituted Enamides.

Enamides represent bioactive pharmacophores in various natural products, and have become increasingly common reagents for asymmetric incorporation of nitrogen functionality. Yet the synthesis of the requisite geometrically defined enamides remains problematic, especially for highly substituted and Z-enamides. Herein we wish to report a general atom economic method for the isomerization of a broad range of N-allyl amides to form Z-di-, tri-, and tetrasubstituted enamides with exceptional geometric selectivity. This report represents the first examples of a catalytic isomerization of N-allyl amides to form nonpropenyl disubstituted, tri- and tetrasubstituted enamides with excellent geometric control. Applications of these geometrically defined enamides toward the synthesis of cis vicinal amino alcohols and tetrasubstituted α-borylamido complexes are discussed.

α-Aminoxy Peptoids: A Unique Peptoid Backbone with a Preference for cis-Amide Bonds.

α-Peptoids, or N-substituted glycine oligomers, are an important class of peptidomimetic foldamers with proteolytic stability. Nevertheless, the presence of cis/trans-amide bond conformers, which contribute to the high flexibility of α-peptoids, is considered as a major drawback. A modified peptoid backbone with an improved control of the amide bond geometry could therefore help to overcome this limitation. Herein, we have performed the first thorough analysis of the folding propensities of α-aminoxy peptoids (or N-substituted 2-aminoxyacetic acid oligomers). To this end, the amide bond geometry and the conformational properties of a series of model α-aminoxy peptoids were investigated by using 1D and 2D NMR experiments, X-ray crystallography, natural bond orbital (NBO) analysis, circular dichroism (CD) spectroscopy, and molecular dynamics (MD) simulations revealing a unique preference for cis-amide bonds even in the absence of cis-directing side chains. The conformational analysis based on the MD simulations revealed that α-aminoxy peptoids can adopt helical conformations that can mimic the spatial arrangement of peptide side chains in a canonical α-helix. Given their ease of synthesis and conformational properties, α-aminoxy peptoids represent a new member of the peptoid family capable of controlling the amide isomerism while maintaining the potential for side-chain diversity.

Structure-activity relationship study and discovery of indazole 3-carboxamides as calcium-release activated calcium channel blockers

Aberrant activation of mast cells contributes to the development of numerous diseases including cancer, autoimmune disorders, as well as diabetes and its complications. The influx of extracellular calcium via the highly calcium selective calcium-release activated calcium (CRAC) channel controls mast cell functions. Intracellular calcium homeostasis in mast cells can be maintained via the modulation of the CRAC channel, representing a critical point for therapeutic interventions. We describe the structure-activity relationship study (SAR) of indazole-3-carboxamides as potent CRAC channel blockers and their ability to stabilize mast cells. Our SAR results show that the unique regiochemistry of the amide linker is critical for the inhibition of calcium influx, the release of the pro-inflammatory mediators β-hexosaminidase and tumor necrosis factor α by activated mast cells. Thus, the indazole-3-carboxamide 12d actively inhibits calcium influx and stabilizes mast cells with sub-μM IC50. In contrast, its reverse amide isomer 9c is inactive in the calcium influx assay even at 100μM concentration. This requirement of the specific 3-carboxamide regiochemistry in indazoles is unprecedented in known CRAC channel blockers. The new structural scaffolds described in this report expand the structural diversity of the CRAC channel blockers and may lead to the discovery of novel immune modulators for the treatment of human diseases.

ChemInform Abstract: N′‐Acylation of (3,2′)‐Indole Dimers.

N-Acylated indoles are abundant in nature, and have much biological importance. In the present investigation, we synthesize homo- and mixed-indole dimers (1, 5) derived from indole and 2-methylindole. N-Acylation of the indoline unit was then performed using triethylamine with acetyl chloride or benzoyl chloride or vinylogues thereof (9a–f). The resulting amides, (10a–f) and (11a–f), 10 of which are novel, could be of synthetic and biological interest. Acylation yields ranged from 50% to 91%, with most examples above 80%. The best results were obtained when base was slowly added to a mixture of indole dimer hydrochloride and acyl chlorides. When crotonoyl or sorboyl chloride was added to a basic solution of indole dimer, the product mixtures included small amounts of isomeric amides. These probably form by ketenes produced by conjugate elimination of HCl from the acyl chloride. No process was found by which the ketene-derived isomers could be obtained in good yield, or quantitatively separated from amides (10) or (11).

N′-Acylation of (3,2′)-indole dimers

N-Acylated indoles are abundant in nature, and have much biological importance. In the present investigation, we synthesize homo- and mixed-indole dimers (1, 5) derived from indole and 2-methylindole. N-Acylation of the indoline unit was then performed using triethylamine with acetyl chloride or benzoyl chloride or vinylogues thereof (9a–f). The resulting amides, (10a–f) and (11a–f), 10 of which are novel, could be of synthetic and biological interest. Acylation yields ranged from 50% to 91%, with most examples above 80%. The best results were obtained when base was slowly added to a mixture of indole dimer hydrochloride and acyl chlorides. When crotonoyl or sorboyl chloride was added to a basic solution of indole dimer, the product mixtures included small amounts of isomeric amides. These probably form by ketenes produced by conjugate elimination of HCl from the acyl chloride. No process was found by which the ketene-derived isomers could be obtained in good yield, or quantitatively separated from amides (10) or (11).

Cs2CO3-Catalyzed Synthesis of N-Sulfonyl-Substituted Allenamides

Several novel N-sulfonyl substituted allenamides were obtained in good yields via Cs2CO3-catalyzed isomerization of propargyl amides in THF at room temperature. The easily available starting materials and mild reaction conditions are features of this protocol.

Serine effects on collision-induced dissociation and photodissociation of peptide cation radicals of the z+●-type

The serine residue displays specific effects on the dissociations of peptide fragment cation-radicals of the z+• type which are produced by electron transfer dissociation. Energy-resolved collision-induced dissociation (ER-CID), time-resolved infrared multiphoton dissociation (TR-IRMPD), and single-photon UV photodissociation at 355 nm revealed several competitive dissociation pathways consisting of loss of OH radical, water, and backbone cleavages occurring at N-terminal and C-terminal positions relative to the serine residue. The activation modes using slow-heating and UV photon absorption resulted in different relative intensities of fragment ions. This indicated that the dissociations proceeded through several channels with different energy-dependent kinetics. The experimental data were interpreted with the help of electron structure calculations that provided fully optimized structures and relative energies for cis and trans amide isomers of the z4+• ions as well as isomerization, dissociation, and transition state energies. UV photon absorption by the z4+• ions was due to Cα-radical amide groups created by ETD that provided a new chromophore absorbing at 355 nm.