Kinetics and equilibria of cis/trans isomerization of backbone amide bonds in peptoids

The biological activities of N-substituted glycine oligomers (peptoids) have been the subject of extensive research. As compared to peptides, both the cis and trans conformations of the backbone amide bonds of peptoids can be significantly populated. Thus, peptoids are mixtures of configurational isomers, with the number of isomers increasing by a factor of 2 with each additional monomer residue. Here we report the results of a study of the kinetics and equilibria of cis/trans isomerization of the amide bonds of N-acetylated peptoid monomers, dipeptoids, and tripeptoids by NMR spectroscopy. Resonance intensities indicate the cis conformation of the backbone amide bonds of the peptoids studied is more populated than is generally the case for the analogous secondary amide bond to proline residues in acyclic peptides. Rate constants were measured by inversion-magnetization transfer techniques over a range of temperatures, and activation parameters were derived from the temperature dependence of the rate constants. The rate of cis/trans isomerization by rotation around the amide bonds in the peptoids studied is generally slower than that around amide bonds to proline residues and takes place on the NMR inversion-magnetization transfer time scale only by rotation around the amide bond to the C-terminal peptoid residue.     

The click triazolium peptoid side chain: a strong cis-amide inducer enabling chemical diversity

Access to homogeneous and discrete folded peptoid structures primarily depends on control of the cis/trans isomerism of backbone tertiary amides. This can be achieved by designing specific side chains capable of forming local interactions with the backbone. This is often undertaken at the expense of side-chain diversity, which is a key advantage of peptoids over other families of peptidomimetics. We report for the first time a positively charged triazolium-type side chain that does not compromise diversity and exhibits the best ability reported to date for inducing the cis conformation. The cis-directing effect was studied in N-acetamide dipeptoid model systems and evaluated in terms of K(cis/trans) using NMR spectroscopy in aprotic and protic solvents. Computational geometry optimization and natural bond orbital analysis in combination with NOESY experiments were consistent with a model in which n → π*(Ar) electronic delocalization [from carbonyl (O(i-1)) to the antibonding orbital (π*) of the triazolium motif on residue i] may be operative. In the computational model (gas-phase) and experimentally in CDCl(3), H-bonding between the triazolium C-H proton and the C(i)═O(i) oxygen was also identified and may act cooperatively with the n → π*(Ar) delocalization, resulting in the absence of the trans rotamers in CDCl(3).     

Studies on novel peptidomimetics having bi-directional dispositions of hydroxylated D-Pro-Gly motifs anchored on a C(2)-symmetric iminosugar-based foundation

A rigid pyrrolidine based scaffold comprising of 2,5-dideoxy-2,5-imino-D-idaric acid (1) is developed. Attachment of peptide strands to the carboxylic groups at both ends of this novel template led to the peptidomimetics 2 and 3. Conformational analysis by NMR studies revealed that compounds 2b, 3b and 2c, 3c take interesting turn structures (C(2) symmetric for 2c and 3c) in DMSO-d(6) consisting of identical intramolecular hydrogen bonds at two ends between LeuNH --> sugar-OH as depicted in structure A, whereas 2a and 3a display structures with regular beta-turns with hydrogen bonds between LeuNH --> Boc-C=O in one-half of their molecular frameworks (structure B), characteristic of the turn structures commonly observed in "D-Pro-Gly"-containing peptides. These results suggest that a cis hydroxyl group at the 3-position of the proline residue favors a pseudo beta-turn-like nine-membered ring structure in hydroxyproline-containing peptides involving an intramolecular hydrogen bond between the hydroxyl and the i + 2 backbone amide.     

Influence of chirality of the preceding acyl moiety on the cis/trans ratio of the proline peptide bond

We report that the cis/trans ratio of the proline peptide bond can be strongly influenced by the chirality of the acyl residue preceding proline. Acyl moieties derived from (2S)-2,6-dimethyl-3-oxo-3,4-dihydro-2H-1,4-benzoxazine-2-carboxylic acid (8) and (2R)-3-methoxy-2-methyl-2-(4-methyl-2-nitrophenoxy)-3-oxopropanoic acid (5) in acyl-Pro molecules influence isomerization of the proline peptide bond constraining the omega dihedral angle to the trans orientation. Structures of benzyl (2S)-1-([(2S)-2,6-dimethyl-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl]carbonyl)-2-pyrrolidinecarboxylate (3) derived from 2D (1)H NMR conformational analysis and crystallographic data exhibit only the trans conformation of proline peptide bond. On the other hand the diastereomer 4, which contains an (R) acyl moiety, exhibits two sets of signals in (1)H NMR spectra. The signals were assigned to trans (72%) and cis (28%) conformers. Crystallographic analysis of 4 showed that only the cis conformation is present in the crystalline state. The (1)H NMR chemical shift pattern of three sets of signals observed in 2 was observed also in benzyl (2S)-1-[(2R/S)-3-methoxy-2-methyl-2-(4-methyl-2-nitrophenoxy)-3-oxopropanoyl]-2-pyrrolidinecarboxylate. (R)-Carboxylic acid 5, after coupling with (S)-ProOBn, yielded benzyl (2S)-1-[(2R)-3-methoxy-2-methyl-2-(4-methyl-2-nitrophenoxy)-3-oxopropanoyl]-2-pyrrolidinecarboxylate (6), which in DMSO-d(6) exhibited only the trans conformation of the proline peptide bond. These results suggest that in these particular cases acyl-Pro peptide bond isomerization is strongly influenced by the stereochemistry of the acyl residue preceding proline. (2S)-2,6-Dimethyl-3-oxo-3,4-dihydro-2H-1,4-benzoxazine-2-carboxylic acid (8) and (2R)-3-methoxy-2-methyl-2-(4-methyl-2-nitrophenoxy)-3-oxopropanoic acid (5) are promising chiral peptidomimetic building blocks that can be used as acyl moieties to force the proline peptide bond into the trans conformation in a variety of acyl-Pro molecules.     

Conformationally locked isostere of phosphoSer-cis-Pro inhibits Pin1 23-fold better than phosphoSer-trans-Pro isostere

Stereoisomeric cis and trans substrate analogues for Pin1 were designed and synthesized. The central phosphoSer-Pro core of the Pin1 substrate was replaced by cis and trans amide isosteres in Ac-Phe-Phe-pSer-Psi[(Z and E)CH=C]-Pro-Arg-NH(2), 1 and 2, peptidomimetics. They were synthesized on solid phase in 17% yield for the cis analogue 1, and 16% yield for the trans analogue 2. A second trans amide isostere with a C-terminal N-methylamide 3 was synthesized in 7% yield. The protease-coupled Pin1 assay showed that all three compounds inhibited the Pin1 peptidyl-prolyl isomerase (PPIase) enzymatic activity. The cis isostere 1 was 23 times more potent (K(i) = 1.74 +/- 0.08 muM) than its trans counterpart 2 (K(i) = 40 +/- 2 muM) in competitive inhibition of Pin1. These results suggest that the catalytic site of Pin1 binds cis substrates more tightly in aqueous solution. Antiproliferative activity toward the A2780 human ovarian cancer cell line by the cis and trans analogues correlates with Pin1 inhibition results.     

Stabilising Peptoid Helices Using Non‐Chiral Fluoroalkyl Monomers

Stability towards protease degradation combined with modular synthesis has made peptoids of considerable interest in the fields of chemical biology, medicine, and biomaterials. Given their tertiary amide backbone, peptoids lack the capacity to hydrogen‐bond, and as such, controlling secondary structure can be challenging. The incorporation of bulky, charged, or chiral aromatic monomers can be used to control conformation but such building blocks limit applications in many areas. Through NMR and X‐ray analysis we demonstrate that non‐chiral neutral fluoroalkyl monomers can be used to influence the K_cis/trans equilibria of peptoid amide bonds in model systems. The cis‐isomer preference displayed is highly unprecedented given that neither chirality nor charge is used to control the peptoid amide conformation. The application of our fluoroalkyl monomers in the design of a series of linear peptoid oligomers that exhibit stable helical structures is also reported.     

Theoretical conformational analysis of the methylamides of N-acetyl-L-alanyl-L-proline and N-acetyl-L-prolyl-L-alanine. I

Summary 1. The most preferred forms of the compounds Ac-L-Ala-L-Pro-NHMe participating in a conformational equilibrium are characterized by both the trans and the cis configurations of the tertiary amide group.2. The formation of intramolecular hydrogen bonds in the conformations of Ac-L-Ala-L-Pro-NHMe realized is unlikely.3. The conformational states of the compounds Ac-L-Pro-L-Ala-NHMe with the trans configurations of the tertiary amide group are most probable. In nonpolar media a probability of the formation of structures with hydrogen bonds is high.4. The conformational distribution of the fragments -X-Pro- and -Pro-X- in proteins agrees satisfactorily with the calculated values of the energy of the optimum forms of the corresponding dipeptides, Ac-L-Ala-L-Pro-NHMe and Ac-L-Pro-L-Ala-NHMe.M. M. Shemyakin Institute of Bioorganic Chemistry, Academy of Sciences of the USSR. Translated from Khimiya Prirodnykh Soedinenii, No. 5, pp. 618–626, September–October, 1975.     

Acid-induced conformational alteration of cis-preferential aromatic amides bearing N-methyl-N-(2-pyridyl) moiety

A series of cis-preferential aromatic N-methyl amides was designed and synthesized, and acid-induced conformational alteration of these compounds was investigated by means of NMR measurements in solution and X-ray crystal structure analysis. Compounds with a terminal N-methyl-N-(2-pyridyl) amide unit showed acid-induced conformational change from cis to trans, while those with a terminal N-methyl-2-pyridinecarboxamide unit showed a change of the carbonyl orientation from anti to syn with retention of cis conformation.     

Extraordinarily robust polyproline type I peptoid helices generated via the incorporation of α-chiral aromatic N-1-naphthylethyl side chains

Peptoids, or oligomers of N-substituted glycines, are a class of foldamers that have shown extraordinary functional potential since their inception nearly two decades ago. However, the generation of well-defined peptoid secondary structures remains a difficult task. This challenge is due, in part, to the lack of a thorough understanding of peptoid sequence-structure relationships and, consequently, an incomplete understanding of the peptoid folding process. We seek to delineate sequence-structure relationships through the systematic study of noncovalent interactions in peptoids and the design of novel amide side chains capable of such interactions. Herein, we report the synthesis and detailed structural analysis of a series of (S)-N-(1-naphthylethyl)glycine (Ns1npe) peptoid homo-oligomers by X-ray crystallography, NMR spectroscopy, and circular dichroism (CD) spectroscopy. Four of these peptoids were found to adopt well-defined structures in the solid state, with dihedral angles similar to those observed in polyproline type I (PPI) peptide helices and in peptoids with α-chiral side chains. The X-ray crystal structure of a representative Ns1npe tetramer revealed an all cis-amide helix, with approximately three residues per turn, and a helical pitch of approximately 6.0 ?. 2D-NMR analysis of the length-dependent Ns1npe series showed that these peptoids have very high overall backbone amide K(cis/trans) values in acetonitrile, indicative of conformationally homogeneous structures in solution. Additionally, CD spectroscopy studies of the Ns1npe homo-oligomers in acetonitrile and methanol revealed a striking length-dependent increase in ellipticity per amide. These Ns1npe helices represent the most robust peptoid helices to be reported, and the incorporation of (S)-N-(1-naphthylethyl)glycines provides a new approach for the generation of stable helical structure in this important class of foldamers.     

Photoinduced gelation by stilbene oxalyl amide compounds

Oxalyl amide derivatives bearing 4-dodecyloxy-stilbene as a cis-trans photoisomerizing unit were synthesized. The trans derivative acted as a versatile gelator of various organic solvents, whereas the corresponding cis derivative showed a poor gelation ability or none at all. In diluted solution (c = 2.0 x10(-5) mol dm(-3), ethanol), the cis isomer was photochemically converted into the trans isomer within 4 min. Depending on the radiation wavelength, the trans isomer was stable or liable to photodecomposition. When exposed to irradiation, a concentrated solution of the cis isomer (c = 2.0 x 10(-2) mol dm(-3), ethanol) turned into a gel. The FT-Raman, FT-IR, and 1H NMR spectra demonstrated that the gelation process occurred because of a rapid cis --> trans photoisomerization followed by a self-assembly of the trans molecules. Apart from the formation of hydrogen bonding between the oxalyl amide parts of the molecules, confirmed by FT-IR spectroscopy, it was assumed that the pi-pi stacking between the trans-stilbene units of the molecule and a lipophilic interaction between long alkyl chains were the interactions responsible for gelation.     

Synthesis, stereochemistry, and reactions of 2,5-diphenylsilacyclopentenes

1,1-Disubstituted derivatives of 2,5-diphenylsilacyclopent-3-enes, namely those having the 1,1-diphenyl, 1,1-dimethyl, 1-alkoxy-1-methyl and 1,1-dialkoxy, were prepared by a one-pot reaction of (1E, 3E)-1,4-diphenyl-1,3-butadiene and dichlorosilanes in the presence of magnesium. Each silacyclopentene was formed as a mixture of one trans and two cis isomers. 1-Ethoxy-1-methyl-2,5-diphenylsilacyclopent-3-ene and 1,1-diethoxy-2,5-diphenylsilacyclopent-3-ene were reacted with optically active alcohols to furnish the corresponding diastereomers. The absolute configuration of one of these diastereomers was determined by X-ray structure analysis. The mixture of cis and trans diastereomers was lithiated by lithium diisopropylamide (LDA) to obtain the trans forms selectively, with the stereoselectivity being determined by NOE experiments.     

Chair/Twist-Boat Energy Gap in Monocyclic, Conformationally Unconstrained Polyalkylcyclohexanes

A conformational search procedure (HUNTER), in combination with the MM3(92) program, was used for the exploration of the conformational hypersurface of alkyl-substituted cyclohexanes and for the calculation of their chair/twist-boat (TB) energy gap. The systems studied were conformationally unconstrained polyalkylcyclohexanes (alkyl = methyl, ethyl, isopropyl, and tert-butyl) possessing either geminal and/or vicinal arrangements of the alkyl groups, but differing in the number of alkyl substituents and in their relative disposition (i.e., cis or trans). The calculations indicate that in 1,1,3,3,5,5-hexaisopropylcyclohexane the TB is the lowest energy form. Modification of the cis,trans relationship of vicinal alkyl groups changes the chair/TB energy gap, and in the minimum energy conformation of cis,trans,trans-1,2,3,4-tetraisopropylcyclohexane (23c) and cis,syn,cis-1,2,4,5-tetraisopropylcyclohexane (31c) the cyclohexyl ring adopts a TB conformation. The tetrasubstituted systems cis,syn,cis-1,2-diisopropyl-3,4-dimethylcyclohexane (46), cis,syn,cis-1,4-diisopropyl-2,5-dimethyl-cyclohexane (47), and cis,trans,trans-1,2-diisopropyl-3,4-dimethylcyclohexane (41) are the least crowded monocyclic unconstrained cyclohexanes found in which the TB conformation is of lower energy than the chair form. The present study indicates that two methyls and two isopropyl substituents are sufficient for stabilizing the TB form of a cyclohexyl ring relative to the chair form.     

cis,cis- and trans,trans-ceratospongamide, new bioactive cyclic heptapeptides from the Indonesian red alga Ceratodictyon spongiosum and symbiotic sponge Sigmadocia symbiotica

Chemical investigation of the marine red alga (Rhodophyta) Ceratodictyon spongiosum containing the symbiotic sponge Sigmadocia symbiotica collected from Biaro Island, Indonesia, yielded two isomers of a new and bioactive thiazole-containing cyclic heptapeptide, cis,cis-ceratospongamide (1) and trans, trans-ceratospongamide (2). Isolation of these peptides was assisted by bioassay-guided fractionation using a brine shrimp toxicity assay (Artemia salina). The structures of the ceratospongamides, which each consist of two L-phenylalanine residues, one (L-isoleucine)-L-methyloxazoline residue, one L-proline residue, and one (L-proline)thiazole residue, were established through extensive NMR spectroscopy, including (1)H-(13)C HMQC-TOCSY, and (1)H-(15)N HMBC experiments, as well as chemical degradation and chiral analysis. cis,cis- and trans,trans-ceratospongamide are stable conformational isomers of the two proline amide bonds. Molecular modeling of these two ceratospongamide isomers showed the trans, trans isomer to be quite planar, whereas the cis,cis isomer has a more puckered overall conformation. trans,trans-Ceratospongamide exhibits potent inhibition of sPLA(2) expression in a cell-based model for antiinflammation (ED(50) 32 nM), whereas the cis,cis isomer is inactive. trans,trans-Ceratospongamide was also shown to inhibit the expression of a human-sPLA(2) promoter-based reporter by 90%.     

13C and 1H NMR of 2,6-diaryl-1-hydroxy piperidin-4-one oximes; substituent effects on cis/trans ratio and conformational equilibria

The reaction of substituted diarylidene acetones with hydroxylamine hydrochloride affords isomeric N-hydroxy diaryl piperidinone oximes as main products. The structures as well as conformational equilibria of these products were established by 1H and 13C NMR spectroscopy and further studied by variable temperature NMR. It was found that the cis/trans ratio of 2,6-substituted piperidine derivatives depended on the position of the substituent on the aromatic ring.     

The impact of pyrrolidine hydroxylation on the conformation of proline-containing peptides

[structure: see text] A series of eight dipeptides of the general formula Ac-Phe-Pro-NHMe was synthesized and the thermodynamics of the cis --> trans isomerization about the central amide bond were studied by NMR. Pro* represents the following prolines: l-proline (Pro), l-trans-4-hydroxyproline (Hyp), l-cis-4-hydroxyproline (hyp), l-cis-4-methoxyproline (hyp[OMe]), l-trans-3-hydroxyproline (3-Hyp), l-cis-3-hydroxyproline (3-hyp), l-2,3-trans-3,4-cis-3,4-dihydroxyproline (DHP), and l-2,3-cis-3,4-trans-3,4-dihydroxyproline (dhp). The conformation of the pyrrolidine ring in each case is discussed in light of previous structural studies, analysis of potential stereoelectronic effects, and NMR data. Hydroxy substituents at C-4 have a greater impact on cis --> trans isomerization than analogous substituents at C-3 as a result of the intervening bond distances and bridging groups. The position of the equilibrium and its dependence on temperature are a reflection of both enthalpic and entropic factors, the latter being complicated in this study by an Ar-Pro interaction in the cis conformation. The substituents on the pyrrolidine ring determine the conformation of the five-membered ring, which in turn influences the strength of the Ar-Pro interaction, backbone dihedral angles, and the relative energy of the cis and trans species. The ultimate position of the equilibrium depends on a complex blend of steric, electronic, and conformational factors.     

4-Methylpseudoproline derived from α-methylserine - synthesis and conformational studies

This paper presents the synthesis and solution conformational studies of the tripeptides Fmoc-Ala-(R)-(αMe)Ser(Ψ(H,H)Pro)-Ala-OBu(t) (6a) and Fmoc-Ala-(S)-(αMe)Ser(Ψ(H,H)Pro)-Ala-OBu(t) (6b). Additionally, the X-ray structure of 6a is given. NMR analysis corroborated by theoretical calculations (XPLOR) shows that in both peptides the amide bond between pseudoproline and the preceding amino acid is in the trans conformation. The same amide bond geometry was observed in the crystal state of 6a. The latter is additionally influenced by the presence of two symmetrically independent molecules in an asymmetric unit. Both molecules adopt a conformation which resembles β-turn type II, stabilized by hydrogen bonding. The conformational preferences and prolyl cis-trans isomerization of Ac-(αMe)Ser(Ψ(H,H)Pro)-NHMe (7) were explored at the IEFPCM/B3LYP/6-31+G(d) level of theory in vacuum, water and chloroform. It has been shown that the trans isomer predominates in water solutions and the cis isomer is preferred in chloroform. The conformation of 7 is down-puckered independently of the geometry of the amide bonds, with lower puckering in the transition state of the cis-trans isomerization.     

A hydrogen-bonding-modulated molecular rotor: environmental effect in the conformational stability of peptidomimetic macrocyclic cyclophanes

The conformational behavior of 16- to 18-membered ring peptidomimetic p-cyclophanes 1a,b-3a,b has been studied by NMR. The cycles bearing 16 and 17 atoms showed a dynamic process within the NMR time scale, produced by the rotation of the aromatic p-diphenylene moiety with respect to the macrocyclic main plane. The temperature dependence of 1H NMR spectra has been studied in order to get activation parameters of the energetic barrier for the process (VT-NMR and line shape analysis). The rate of the movement clearly depends on the macrocyclic ring size and the nature of the peptidomimetic side chain. Entropic and enthalpic contributions to the free energy of activation are discussed. The rotation of the aromatic ring is closely related to the intramolecular hydrogen bonding pattern, as suggested by temperature factors of NH chemical shifts (DeltadeltaNH/DeltaT) and molecular modeling. The interconnected roles of the solvation and the intramolecular H-bonds have been established by measurements (VT-NMR and DeltadeltaNH/DeltaT) in environments of different polarities and H-bonding abilities. We concluded that the conformational stability of the systems directly depends on the stability of the intramolecular H-bonding pattern. We finally showed how one of these peptidomimetics behaves as a methanol-dependent artificial molecular rotor. In this simple molecular device, the well-defined molecular rotation is tuned by the competition between intramolecular hydrogen bonds and interactions with the solvent.     

An intramolecular ionic hydrogen bond stabilizes a cis amide bond rotamer of a ring-opened rapamycin-degradation product

Rapamycin (1), a macrolide immunosuppressant, undergoes degradation into ring-opened acid products 2 and 3 under physiologically relevant conditions. The unsaturated product (3) was isolated and studied in this work. Unlike 1, which has its amide primarily in a trans conformation in solution, 3 has both cis and trans conformations in approximately a 1:1 ratio in dimethyl sulfoxide (DMSO). The amount of cis rotamer was increased dramatically in the presence of an organic base such as triethylamine. The detailed NMR results indicate that the cis rotamer is stabilized through an intramolecular ionic hydrogen bond of the carboxylate anion with the tertiary alcohol as part of a nine-membered ring system. This hydrogen bond was characterized further in organic media and the trans-cis rotamer equilibria were used to estimate the relative bond strengths in several solvents. The additional stabilization arising from this ionic hydrogen bond in the cis rotamer was determined to be 1.4 kcal mol(-1) in DMSO-d6, 2.0 kcal mol(-1) in CD3CN and 1.1 kcal mol(-1) in CD3OD.     

An efficient synthesis of N1-substituted 2,5-dioxo-1,2,5,6,7,8-hexahydro-3-quinolinecarboxamide via enolate salts

Various 2-(2-cyano-2-carbamoyl-1-ethenyl)-5,5-dimethyl-3-oxo-1-cyclohexen-1-olates substituted in the amide group with dialkylammonium or sodium cations were prepared via reactions of N-substituted cyanoacetamides with dimedone-DMFDMA adduct by a one-pot, two-step protocol. The salts obtained were used in reactions with N-nucleophiles for further synthesis of the N1-substituted 2,5-dioxo-1,2,5,6,7,8-hexahydro-3-quinolinecarboxamides that are analogues of well-known pharmaceuticals. The structure of the salts and the N1-substituted 2,5-dioxo-1,2,5,6,7,8-hexahydro-3-quinolinecarboxamides was established by means of spectroscopic and X-ray diffraction studies.     

Organic crystal engineering with 1,4-piperazine-2,5-diones. 6. Studies of the hydrogen-bond association of cyclo[(2-methylamino-4,7-dimethoxyindan-2-carboxylic acid)(2-amino-4,7-dimethoxyindan-2-carboxylic acid)

[structure: see text] The title 1,4-piperazine-2,5-dione was synthesized in 23% yield over six steps from ethyl 2-amino-4,7-dimethoxyindan-2-carboxylate. Crystallization by slow diffusion of ether into a chloroform solution and by slow evaporation of an ethanol-chloroform-benzene solution produced polymorphic crystalline forms as determined by single-crystal X-ray analysis. The polymorphs exhibited different hydrogen-bonding networks. The association of this piperazinedione in solution was studied using mass spectrometric and nuclear magnetic resonance spectroscopic techniques. The MS and NMR data were interpreted using the solid-state structures as models for solution aggregation. Association constants extracted from the NMR data are in line with those of other cyclic cis amides in chloroform solvent.