Isomerization amide bond

A peptoid pentamer of five poro-substituted (S)-N-(l-phenylethyl)glycine monomers, which exhibits the characteristic a-helix-like CD spectrum described above, was further analyzed by 2D-NMR [42]. Although this pentamer has a dynamic structure and adopts a family of conformations in methanol solution, 50-60% of the population exists as a right-handed helical conformer, containing all cis-amide bonds (in agreement with modeling studies [3]), with about three residues per turn and a pitch of 6 A. Minor families of conformational isomers arise from cis/trans-amide bond isomerization. Since many peptoid sequences with chiral aromatic side chains share similar CD characteristics with this helical pentamer, the type of CD spectrum described above can be considered to be indicative of the formation of this class of peptoid helix in general. 

And most importantly for a discussion of the replacement of amide bonds by fluoroolefin isosteres, the cis and trans amide bonds have different hydration shells [43,85]. The role of solvation and desolvation is understood to be crucial not only in amide bond isomerization but also in peptide transport generally. 

Intramolecular catalysis of amide bond isomerization is believed to play a key role in the folding of several proteins and this process has now been demonstrated experimentally including evidence for an H-bond between the side-chain and the prolyl Na in a cis-proline peptidomimetic.143 The amide (178) and the ester (179) have been used as substrates for these studies. Support for intramolecular nucleophilic attack... 

Amide bond isomerizations are faster in nonpolar solvents than in water (Drakenberg et al., 1972), probably because the transition state... 

The prolyl isomerases catalyze isomerizations only at prolyl bonds and not at nonprolyl peptide bonds. The refolding of the P39A variant of RNase Tl, which is limited in rate by the very slow trans —> cis reisomerization of the Tyr38-Ala39 bond (see Section IV.B), is not catalyzed by cyclophilins, FKBPs, or parvulins. These enzymes are also unable to catalyze amide bond isomerizations in the proline-free model peptide Ala-Ala-Tyr-Ala-Ala (Scholz etal., 1998b). 

As a further application of the reaction, the conversion of an endocyclic double bond to an c.xo-methylene is possible[382]. The epoxidation of an cWo-alkene followed by diethylaluminum amide-mediated isomerization affords the allylic alcohol 583 with an exo double bond[383]. The hydroxy group is eliminated selectively by Pd-catalyzed hydrogenolysis after converting it into allylic formate, yielding the c.ro-methylene compound 584. The conversion of carvone (585) into l,3-disiloxy-4-methylenecyclohexane (586) is an example[382]. 

Moreover, when carbamino and nitro groups are simultaneously in the ortho position to the triple bond, isomerization occurs only with participation of the amide group (Scheme 125). 

Nevertheless, the adjacent position of the amide and acetylenic groups was used in another type of heterocyclization. The nitrogen atom in the amide group is a weak nucleophile. Therefore, the N anion should be generated by potassium ethoxide. There are two possible variants of nucleophilic addition to the triple bond. Only one takes place, i.e., the formation of y-lactam. After 7 h of heating in EtOH in the presence of KOH, amide 72 isomerized into the known isoindoline 73 in 80% yield (Scheme 128). 

If peptide residues are converted to peptoid residues, the conformational heterogeneity of the polymer backbone is likely to increase due to cis/trans isomerization at amide bonds. This will lead to an enhanced loss of conformational entropy upon peptoid/protein association, which could adversely affect binding thermodynamics. A potential solution is the judicious placement of bulky peptoid side chains that constrain backbone dihedral angles. 

In the last 5 years, catalytic antibodies have been generated for several reaction types, including the various types of hydrolysis, transesterification, amide bond formation, /3-elimination, cycloreversion, transacylation, redox reactions, E-Z isomerization, epoxidation, and Diels-Alder reactions. For more information on these and other recent developments, such as semi-synthetic antibodies, site-directed mutagenesis, and the bait-and-switch strategy, the reader should consult the appropriate authorities (Schultz, 1988, 1989a,b Benkovic et al., 1990 Janda et al., 1990, 1991 Janjic and Tramontano, 1990 Lerner et al., 1991). 

Two structurally unrelated immunosuppressant drugs, cyclosporin A and FK506, have been shown to bind to separate proteins, which have in common the ability to catalyse the interconversion (8) of the cis and trans rotamers of peptidyl-proline bonds of peptide substrates. A profound change in the conformation, and hence the shape and binding properties of the protein, may result. The mechanism of this isomerization appears, on the basis of recent work (Rosen et al., 1990 Van Duyne et al., 1993 Albers et al., 1990), to involve simple twisting about the amide bond, rather than such alternatives as conversion to a C-N single bond by addition of a nucleophile to C=0.y The proteins which catalyse the reaction may be... 

The rate law for the oxidation of [Ru(NH3)5(FlL)] + (HE = isonicotinamide) by I2 in acidic solution contains two terms, one depending on P2] and one depending on [I3 ] and [Ru complex]. An outer-sphere electron-transfer mechanism is proposed for each term. Reduction of [Ru (NFl3)5L] + (TIL = nicotinamide or isonicotinamide) to [Ru (NH3)5L]+ is accompanied by an isomerization from the amide-bonded L to pyridine-bonded FIL. Bromine oxidation of... 

Tertiary amides, such as those associated with prolyl amide bonds frequently influence turn architectures. The importance of the cis Xaa-Pro bond on activity was recognized and proposed to be the source of differentiation in biological activity [86] therefore, isomerization of the prolyl amide bond is central to regulation of protein folding, immunosuppression, and mitosis. These functions are not surprisingly associated with several disease states and thus substitution of the acyl-proline amide bond with the fluoroolefin isostere has received considerable attention. 

The mechanism of the aminolysis and the electronic effects of substituents at C-2 or C-4 on the kinetics of amide bond formation have been studied. In some cases, ring opening with amines occurs with partial isomerization of the exocyclic double bond. However, with more hindered compounds, such as unsaturated oxazolones derived from ketones, ring opening is stereospecific.Ring opening using diamines has also been described. Selected examples of dehydroamino acid amides prepared by aminolysis of unsaturated 5(4//)-oxazolones are shown in Table 7.40 (Fig. 7.51). 

Each of the scaffolds reported in Scheme 24 can be used for the production of a stereo-isomeric sublibrary based on the appropriate peptide sequence. For example, with the sequence A-B-C-D-E and scaffold (1) two types of stereoisomeric sublibraries can be prepared. One type includes the sublibraries A and B of Scheme 26 in which within a given sequence the configuration of each residue is successively inverted thus, retaining the identical connectivity as in the parent linear peptide. In the second type 265 of sublibraries C and D (Scheme 26) the direction of the amide bond is inverted and hence the connectivity is not maintained. In most members of these sublibraries the overall conformation of the scaffold is maintained and therefore these components constitute stereoisomeric sublibraries of the parent library. Conversely, by introducing amide bond surrogates such as reduced amide bonds1465 or thioamide bonds 260,466 the conformation of the scaffolds are changed and their conformational flexibility enhanced. 

The Z-alkene isostere mimics the cis-amide bond conformation. Its molecular volume and log p values are almost identical to those of the E-isostere (Table 1). Its use in bioactive peptides is very limited, probably because of the synthetic challenge involved. One study reports the migration of the double bond to the a,(3-position in an enkephalin analogue. 4 The Z-alkene in the Alat t[Z, CH=CH]Pro dipeptide isostere, however, was reported to be stable towards isomerization.1 1X1 orf/to-Substituted aromatic or tetrazole rings have been used more frequently as ds-amide bond mimics. 

An ab initio method has been employed to study the mechanism of the thermal isomerization of buta-1,2-diene to buta-1,3-diene. The results of the study have indicated619 that the transformation proceeds in a stepwise manner via a radical intermediate. Experimental free energies of activation for the bond shift in halocyclooctatetraenes have been reported and analyzed by using ab initio MO calculations.620 The isomerization of hexene using a dihydridorhodium complex in dimethyl sulfoxide has been reported,621 and it has been suggested622 that the Pd(II)-catalysed homogeneous isomerization of hexenes proceeds by way of zr-allylic intermediates. A study has been made623 of alkene isomerization catalysed by the rhodium /-phosphine-tin dichloride dimeric complex, and the double-bond isomerization of olefinic amines over potassium amide loaded on alumina has been described.624... 

The effect of organic solvents on the rate constant for amide rotation in Af,A -dimethylacetamide (DMA) has also been investigated (Drakenberg et ai, 1972). As the solvent is changed from water to acetone to cyclohexane, first-order rate constants for rotation increase from 0.025 to 0.33 to 1.5 sec . This observation that nonpolar solvents increase reaction rates indicates that the transition state for amide rotation is nonpolar relative to the reactant state and, thus, is stabilized in nonpolar solvents. This transition state is presumably characterized by partial rotation about the amide bond. In this transition state, polar resonance structures for the amide bond no longer exist and, thus, the transition state is less polar than the reactant state. The 60-fold rate acceleration that accompanies transfer of DMA from water to cyclohexane will provide an important clue in understanding enzymatic prolyl isomerization (see below). 

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