Structural analysis of a beta-helical protein motif stabilized by targeted replacements with conformationally constrained amino acids

Here we study conformational stabilization induced in a beta-helical nanostructure by position-specific mutations. The nanostructure is constructed through the self-assembly of the beta-helical building block excised from E. coli galactoside acetyltransferase (PDB code 1krr , chain A; residues 131-165). The mutations involve substitutions by cyclic, conformationally constrained amino acids. Specifically, a complete structural analysis of the Pro-Xaa-Val sequence [with Xaa being Gly, Ac 3c (1-aminocyclopropane-1-carboxylic acid) and Ac 5c (1-aminocyclopentane-1-carboxylic acid)], corresponding to the 148-150 loop region in the wild-type (Gly) and mutated (Ac 3c and Ac 5c) 1krr , has been performed using Molecular Dynamics simulations and X-ray crystallography. Simulations have been performed for the wild-type and mutants of three different systems, namely the building block, the nanoconstruct and the isolated Pro-Xaa-Val tripeptide. Furthermore, the crystalline structures of five peptides of Pro-Xaa-Val or Xaa-Val sequences have been solved by X-ray diffraction analysis and compared with theoretical predictions. Both the theoretical and crystallographic studies indicate that the Pro-Ac n c-Val sequences exhibit a high propensity to adopt turn-like conformations, and this propensity is little affected by the chemical environment. Overall, the results indicate that replacement of Gly149 by Ac 3c or Ac 5c significantly reduce the conformational flexibility of the target site enhancing the structural specificity of the building block and the nanoconstruct derived from the 1krr beta-helical motif.     

Peptide backbone folding induced by the C(alpha)-tetrasubstituted cyclic alpha-amino acids 4-amino-1,2-dithiolane-4-carboxylic acid (Adt) and 1-aminocyclopentane-1-carboxylic acid (Ac5c). A joint computational and experimental study

The conformational study of a new group of synthetic peptides containing 4-amino-1,2-dithiolane-4-carboxylic acid (Adt), a cysteine-related achiral residue, has been carried out through a joint application of computational and experimental methodologies. Molecular Dynamics simulations clearly suggest the tendency of this molecule to adopt a gamma-turn conformation in vacuum and help in analyzing the complex and crucial conformational behaviour of the dithiolane ring which appears to preferentially adopt a C(S)-like structure. Electronic structure calculations carried out in solution using the Density Functional Theory also indicate the preservation of the gamma-like folding in apolar solvents and the helix-like one in more polar solvents. A comparison with the achiral 1-aminocycloalkane-1-carboxylic acid (Ac5c) has been carried out using the same computational tools. NMR and IR data on dipeptide derivatives containing the Adt or Ac5c residue show that in chloroform solution all the models prefer a gamma-turn structure, centered at the cyclic residue, stabilized by an intramolecular H-bond, whereas in a more polar solvent, i.e. dimethyl sulfoxide, this folding is not maintained. The experimental conformational studies, extended to N-Boc protected tripeptides, clearly indicate the remarkable tendency of both the five-membered C(alpha)-tetrasubstituted cyclic amino acids Adt and Ac5c to induce the gamma-turn structure also in models able to adopt the beta-bend conformation.     

The singular gas-phase structure of 1-aminocyclopropanecarboxylic acid (Ac3c)

The natural nonproteinogenic α-amino acid 1-aminocyclopropanecarboxylic acid (Ac(3)c) has been vaporized by laser ablation and studied in the gas phase by molecular-beam Fourier transform microwave spectroscopy. Comparison of the experimental rotational and (14)N nuclear quadrupole coupling constants with the values predicted ab initio for these parameters has allowed the unambiguous identification of three Ac(3)c conformers differing in the hydrogen bonding pattern. Two of them resemble those characterized before for the coded aliphatic α-amino acids. Remarkably, a third conformer predicted to be energetically accessible for all of these amino acids but never observed (the so-called "missing conformer") has been found for Ac(3)c, close in energy to the global minimum. This is the first time that such a conformer, stabilized by an N-H···O(H) hydrogen bond, is detected in the rotational spectrum of a gaseous α-amino acid with a nonpolar side chain. The conjugative interaction established between the cyclopropane ring and the adjacent carbonyl group seems to be responsible for the unique conformational properties exhibited by Ac(3)c.     

Chemical communication: conductors and insulators of screw-sense preference between helical oligo(aminoisobutyric acid) domains

(1)H NMR studies quantify the abilities of achiral amino acids to communicate a left-handed screw-sense preference from one helical Aib(4) domain to another: certain quaternary amino acids (e.g. Ac(6)c) act as effective conductors of conformational preference while others (e.g. diphenylglycine) acts as insulators.     

1-amino-2-phenylcyclopentane-1-carboxylic acid: a conformationally restricted phenylalanine analogue

DFT calculations at the B3LYP/6-311G(d,p) level have been used to investigate the intrinsic conformational preferences of 1-amino-2-phenylcyclopentane-1-carboxylic acid (c5Phe), a constrained analogue of phenylalanine in which the alpha and beta carbons are included in a cyclopentane ring. Specifically, the N-acetyl-N'-methylamide derivatives of the cis and trans stereoisomers, where cis and trans refer to the relative position between the amino group and the phenyl ring, have been calculated. Solvent effects have been examined using a self-consistent reaction field (SCRF) method. Results indicate that the conformational space of the cis stereoisomer is much more restricted than that of the trans derivative both in the gas phase and in solution.     

Diastereoselective synthesis and estimation of the conformational flexibility of 6-oxoperhydropyridazine-3-carboxylic acid derivatives

alpha,beta-Didehydroglutamates have been diastereoselectively transformed into 6-oxoperhydropyridazine-3-carboxylic acid derivatives (OPCAs), which constitute a new class of cyclic amino acid derivatives. Acylation at N-1 renders dipeptides which show considerable conformational rigidity. Semiempirical calculations suggest that OPCAs might force peptide turns with different amplitudes depending on the substitution pattern and relative stereochemistry of the substituents of the pyridazinone ring.     

Design and synthesis of chiral alpha,alpha-disubstituted amino acids and conformational study of their oligopeptides

alpha,alpha-Disubstituted amino acids are alpha-amino acids in which the hydrogen atom at the alpha-position of the L-alpha-amino acid is replaced with an alkyl substituent. The introduction of an alpha-alkyl substituent changes the properties of amino acids, with the conformational freedom of the side chain in the amino acids and the secondary structure of their peptides being especially restricted. The author developed a synthetic route of optically active alpha-ethylated alpha,alpha-disubstituted amino acids using chiral cyclic 1,2-diol as a chiral auxiliary. It was found that the preferred secondary structure of peptides composed of chiral alpha-ethylated alpha,alpha-disubstituted amino acids is a fully extended C5-conformation, whereas that of peptides composed of chiral alpha-methylated alpha,alpha-disubstituted amino acids is a 3(10)-helical structure. Also, a new chiral cyclic amino acid; (3S,4S)-1-amino-3,4-di(methoxy)cyclopentanecarboxylic acid {(S,S)-Ac5c(dOM)}, and a bicyclic amino acid; (1R,6R)-8-aminobicyclo[4.3.0]non-3-ene-8-carboxylic acid {(R,R)-Ab5,6= c}, in which the alpha-carbon atom is not the chiral center but chiral centers exist at the side-chain cycloalkane skeleton, were designed and synthesized. The (S,S)-Ac5c(dOM) hexa- and octapeptides preferentially formed left-handed (M) helices, in which the helical-screw direction is exclusively controlled by the side-chain chiral centers. Contrary to the left-handed helices of (S,S)-Ac(5)c(dOM) peptides, the (R,R)-Ab5,6= c hexapeptide formed both diastereomeric right-handed (P) and left-handed (M) helices, and the twelve chiral centers at the side chain showed no preference for helical-screw direction. Thus, the chiral environment at the side chain is important for the control of helical-screw direction. Furthermore, the author designed a new class of chiral cyclic alpha,alpha-disubstituted amino acids that have pendant chiral centers at the substituent of the delta-nitrogen atom. The synthetic route would provide various optically-active cyclic alpha,alpha-disubstituted amino acids bearing a pendant chiral moiety.     

Derivatives of orotic acid and its analogs

The lactone of 2, 6-dichloro-5-(hydroxymethyl)pyrimidine-4-carboxylic acid is synthesized, and various 2-chloro-6-amino and 2, 6-diamino derivatives are prepared from it by ammonolysis. It is shown that treatment of these compounds with alkaline reagents leads to lactone ring opening when there is a primary or secondary amino group at position 6, while the lactone ring is unaffected if there is a tertiary amino group at that position.A study is made of the action of dilute solutions of hydrochloric acid on the amino derivatives obtained by opening the lactone ring, and their reverse conversion to the corresponding 2, 6-substituted lactones of 5-(hydroxymethyl)pyrimidine-4-carboxylic acid is demonstrated.For Part III see [1].     

Use of constrained synthetic amino acids in beta-helix proteins for conformational control

A highly constrained amino acid has been introduced in the turn region of a beta-helix to increase the conformational stability of the native fold for nanotechnological purposes. The influence of this specific amino acid replacement in the final organization of beta-helix motifs has been evaluated by combining ab initio first-principles calculations on model systems and molecular dynamics simulations of entire peptide segments. The former methodology, which has been applied to a sequence containing three amino acids, has been used to develop adjusted templates. Calculations indicated that 1-amino-2,2-diphenylcyclopropanecarboxylic acid, a constrained cyclopropane analogue of phenylalanine, exhibits a strong tendency to form and promote folded conformations. On the other hand, molecular dynamics simulations are employed to probe the ability of such a synthetic amino acid to enhance the conformational stability of the beta-helix motif, which is the first requirement for further protein nanoengineering. A highly regular segment from a naturally occurring beta-helix protein was selected as a potential nanoconstruct module. Simulations of wild type and mutated segments revealed that the ability of the phenylalanine analogue to nucleate turn conformations enhances the conformational stability of the beta-helix motif in isolated peptide segments.     

Conformational preferences of proline analogues with different ring size

The conformational study on L-azetidine-2-carboxylic acid (Ac-Aze-NHMe, the Aze dipeptide) and (S)-piperidine-2-carboxylic acid (Ac-Pip-NHMe, the Pip dipeptide) is carried out using ab initio HF and density functional methods with the self-consistent reaction field method to explore the differences in conformational preferences and cis-trans isomerization for proline residue and its analogues with different ring size in the gas phase and in solution (chloroform and water). The change of ring size by deleting a CH2 group from or adding a CH2 group to the prolyl ring results the remarkable changes in backbone and ring structures compared with those of the Pro dipeptide, especially in the C'-N imide bond length and the bond angles around the N-C(alpha) bond. The four-membered azetidine ring can have either puckered structure depending on the backbone structure because of the less puckered structure. The six-membered piperidine ring can adopt chair and boat conformations, but the chair conformation is more preferred than the boat conformation. These calculated preferences for puckering are consistent with experimental results from analysis of X-ray structures of Aze- and Pip-containing peptides. On going from Pro to Aze to Pip, the axiality (i.e., a tendency to adopt the axial orientation) of the NHMe group becomes stronger, which can be ascribed to reduce the steric hindrances between 1,2-substituted Ac and NHMe groups. As the solvent polarity increases, the polyproline II-like conformation becomes more populated and the relative stability of conformation tC with a C7 hydrogen bond between C'=O of the amino group and N-H of the carboxyl group decreases for both the Aze and Pip dipeptides, as seen for the Pro dipeptide. The cis population and rotational barriers for the imide bond increase with the increase of solvent polarity for both the Aze and Pip dipeptides, as seen for the Pro dipeptide. In particular, the cis-trans isomerization proceeds in common through only the clockwise rotation with omega' approximately +120 degrees about azetyl and piperidyl peptide bonds in the gas phase and in solution, as seen for alanyl and prolyl peptide bonds. The pertinent distance d(N...H-N(NHMe)) and the pyramidality of imide nitrogen can describe the role of this hydrogen bond in stabilizing the transition state structure, but the lower rotational barriers for the Aze and Pip dipeptides than those for the Pro dipeptide, which is observed from experiments, cannot be rationalized.     

The nitrosation of Amino Acids

With a view to clarifying analogies and differences between the mechanisms involved in the nitrosation of amino acids and secondary amines, we studied the kinetics of the nitrosation of five imino acids (azetidine-2-carboxylic acid, pyrrolidine-2-carboxylic acid, piperidine-2-carboxylic acid, piperidine-3-carboxylic acid, and piperidine-4-carboxylic acid) and of the ethyl esters of three of them. Reaction kinetics were determined by the initial rate method, by spectrophotometric monitoring of the concentration of nitroso amino acid formed. The presence of the ? COO^? group in the amino acids opens a new mechanistic route for the nitrosation of the secondary amino group: a nitrosyl carboxylate formed initially acts as an internal nitrosating agent, resulting in intramolecular migration of ? N ? O from the carboxylate group to the secondary amino group. The observed order of the α?, β?, and γ-amino acids as regards the ease of N-nitrosation by this route is explained in terms of the relative energies of (a) the equatorial and axial orientations of the C_ring? C_carboxyl bond, and (b) the chair and boat forms of the piperidine ring. © 1994 John Wiley & Sons, Inc.     

Substituent effects on the acidity of weak acids. 1. Bicyclo[2.2.2]octane-1-carboxylic acids and bicyclo[1.1.1]pentane-1-carboxylic acids

The acidities of 3- and 4-substituted bicyclooctane-1-carboxylic acids and 3-substituted bicyclo[1.1.1]pentane-1-carboxylic acids have been calculated at the MP2/6-311++G** theoretical level. There is good agreement between the calculated and observed gas-phase acidities. The acidities of the 4-substituted bicyclooctane acids were found to be linearly dependent on the C-X bond dipoles, as expected from a field effect. The substituents had a negligible effect on the electron density at C1. The difference in acidity between 4-chlorobicyclo[2.2.2]octane-1-carboxylic acid and the parent acid (6.2 kcal/mol) is reproduced by the Kirkwood-Westheimer treatment of substituent effects on acidity, but only if the bicyclooctane ring is given an effective dielectric constant of unity. The acidities of the 3-substituted bicyclooctane acids are linearly related to the corresponding 4-substituted acids with a slope of 0.9. The acidities of the 3-substituted bicyclo[1.1.1]pentane-1-carboxylic acids are linearly related to the C-X bond dipoles for this ring system (which are different than those for the bicyclooctanes), and they are also linearly related to the acidity of the 4-substituted bicyclo[2.2.2]octanecarboxylic acids with a slope of 1.34. The larger slope is due to the smaller bridgehead-bridgehead distance in the bicyclopentane ring than in bicyclo[2.2.2]octane.     

Molecular conformation and packing of peptide beta hairpins in the solid state: structures of two synthetic octapeptides containing 1-aminocycloalkane-1-carboxylic acid residues at the i+2 position of the beta turn

Peptide beta-hairpin formation is facilitated by centrally positioned D-Pro-Xxx segments. The synthetic peptides Boc-Leu-Phe-Val-D-Pro-Ac(6)c-Leu-Phe-Val-OMe (1) and Boc-Leu-Phe-Val-D-Pro-Ac(8)c-Leu-Phe-Val-OMe (2) were synthesized in order to explore the role of bulky 1-aminocycloalkane-1-carboxylic acid residues (Ac(n)c, where n is the number of carbon atoms in the ring), at the i+2 position of the nucleating beta turn in peptide beta hairpins. Peptides 1 and 2 crystallize in the monoclinic space group P2(1) with two molecules in the asymmetric unit. The crystal structures of 1 and 2 provide conformational parameters for four peptide hairpin molecules. In all cases, the central segments adopts a type II' beta-turn conformation, and three of the four possible cross-strand hydrogen bonds are observed. Fraying of the hairpins at the termini is accompanied by the observation of NHpi interaction between the Leu(1)NH group and Phe(7) aromatic group. Cross strand stabilizing interactions between the facing residues Phe(2) and Phe(7) are suggested by the observed orientation of aromatic rings. Anomalous far-UV CD spectra observed in solution suggest that close proximity of the Phe rings is maintained even in isolated molecules. In both peptides 1 and 2, the asymmetric unit consists of approximately orthogonal hairpins, precluding the formation of a planar beta-sheet arrangement in the solid state. Solvent molecules, one dioxane and one water in 1, three water molecules in 2, mediate peptide association. A comparison of molecular conformation and packing motifs in available beta-hairpin structures permits delineation of common features. The crystal structures of beta-hairpin peptides provide a means of visualizing different modes of beta-sheet packing, which may be relevant in developing models for aggregates of polypeptides implicated in disease situations.     

Total synthesis of aeruginosin 298-A analogs containing ring oxygenated variants of 2-carboxy-6-hydroxyoctahydroindole

Aeruginosins are a family of naturally occurring oligopeptides sharing a common perhydroindole-2-carboxylic acid (l-Choi) core structure. Many aeruginosins exhibit inhibitory activity against serine proteases including thrombin. Aeruginosin 298-A is a tetrapeptide containing the l-Choi core structure and three other unusual amino acids or their derivatives; it is a thrombin and trypsin inhibitor. As part of our effort in finding effective thrombin inhibitors from natural product analogs and to understand the influence of the rigid bicyclic amino acid to the thrombin inhibition activities, we synthesized two aeruginosin 298-A analogs in which the l-Choi is replaced with ring oxygenated perhydroindole-2-carboxylic acids. The Choi variants are enantiomers synthesized from d- and l-glucose, respectively. The preparation of the aeruginosin 298-A analogs containing the ring oxygenated Choi variants and their inhibition activities toward thrombin and trypsin are reported.     

Highly substituted pyrrolidinones and pyridones by 4-CR/2-CR sequence

[reaction: see text] By combining a Ugi four-component reaction of isocyanides, phosphonoacetic acids, primary amines, and glyoxals or alternatively 3-keto aldehydes with a subsequent Wittig ring-closing reaction (using the Horner/Wadsworth/Emmons variant (HWE)), highly substituted 5-oxo-2,5-dihydro-1H-pyrrole-2-carboxylic acid amides and 6-oxo-1,2,3,6-tetrahydro-pyridine-2-carboxylic acid amides can be assembled, respectively. The corresponding tandem of a Passerini reaction on 3-keto aldehydes and subsequent Wittig ring closure does not afford the expected six-membered 6-oxo-3,6-dihydro-2H-pyran-2-carboxylic acid amides but instead leads to the formation of 4-oxo-pent-2-enoic acid amides via an elimination route.     

Ibotenic acid analogues. Synthesis and biological testing of two bicyclic 3-isoxazolol amino acids

The bicyclic 3-isoxazolol amino acids (RS)-3-hydroxy-4,5,6,7-tetrahydroisoxazolo[4,5-c]pyridine-4-carboxylic acid (5, 4-HPCA) and (RS)-3-hydroxy-4,5,6,7-tetrahydroisoxazolo[4,5-c]pyridine-6-carboxylic acid (11, 6-HPCA) were synthesized as model compounds for studies of the structural requirements of central excitatory amino acid neurotransmitter receptors. 4-HPCA was synthesized via introduction of a methoxycarbonyl group into the 4-position of the lithiated N-nitroso intermediate 1. The key reaction in the synthesis of 6-HPCA is an intramolecular N-alkylation of the appropriately substituted acetamidomalonate derivative 7 using sodium hydride as a base. On the basis of the pKA values for 4-HPCA the existence of an intramolecular hydrogen bond in the zwitterionic form of this amino acid is proposed. 6-HPCA was shown by 1H NMR spectroscopy to adopt preferentially a conformation with the carboxylate group in an equatorial position. 4- and 6-HPCA were tested as agonists and antagonists at excitatory amino acid receptors on neurones in the cat spinal cord using microelectrophoretic techniques. Neither compound showed significant effects at these receptors.     

Electrosynthesis of 4-chloropyrazolecarboxylic acids

4-Chlorosubstituted pyrazolecarboxylic acids were synthesized via chlorination of the corresponding acids at the Pt anode in NaCl aqueous solutions under conditions of divided galvanostatic electrolysis. The efficiency of the process depends on the structures of the initial pyrazolecarboxylic acids, particularly, on the donor-acceptor properties of the substituents and on their position in the pyrazole ring. The yields of the 4-chlorosubstituted products of chlorination of pyrazole-3(5)-carboxylic acid, 1-methylpyrazole-5-carboxylic acid, 1-methyl-pyrazole-3-carboxylic acid, 1-ethylpyrazole-3-carboxylic acid, and 1-methyl-3-nitropyrazole- 5-carboxylic acid are 92, 93, 69, 80, and 4%, respectively.     

Synthesis of bicyclic tertiary alpha-amino acids

Novel bicyclic alpha-amino acids, exo and endo-1-azabicyclo[2.2.1]heptane-2-carboxylic acid, 1-azabicyclo[2.2.1]heptane-7-carboxylic acid, and 1-azabicyclo[3.2.2]nonane-2-carboxylic acid have been readily synthesized for the generation of neuronal nicotinic receptor ligands. Alkylation of glycine-derived Schiff bases or nitroacetates with cyclic ether electrophiles, followed by acid-induced ring opening and cyclization in NH4OH, allowed for the preparation of substantial quantities of the three tertiary bicyclic alpha-amino acids.     

Conformational studies on peptides containing α,α-disubstituted α-amino acids: chiral cyclic α,α-disubstituted α-amino acid as an α-helical inducer

Four types of α,α-disubstituted amino acids {i.e., α-aminoisobutyric acid (Aib), 1-aminocyclopentanecarboxylic acid (Ac(5)c), (3S,4S)-1-amino-(3,4-dimethoxy)cyclopentanecarboxylic acid [(S,S)-Ac(5)c(dOM)] and its enantiomer (R,R)-Ac(5)c(dOM)} were introduced into l-leucine-based hexapeptides and nonapeptides. The dominant conformations of eight peptides: Cbz-(L-Leu-L-Leu-dAA)(2)-OMe [dAA = 1: Aib; 2: Ac(5)c; 3: (S,S)-Ac(5)c(dOM); 4: (R,R)-Ac(5)c(dOM)] and Boc-(L-Leu-L-Leu-dAA)(3)-OMe [dAA = 5: Aib; 6: Ac(5)c; 7: (S,S)-Ac(5)c(dOM); 8: (R,R)-Ac(5)c(dOM)], were investigated by IR, CD spectra and X-ray crystallographic analysis. The CD spectra revealed that Aib hexapeptide 1 and Ac(5)c hexapeptide 2 formed right-handed (P) 3(10)-helices, while Ac(5)c(dOM) hexapeptides 3 and 4 formed a mixture of (P) 3(10)- and α-helices. The Aib nonapeptide 5 formed a (P) 3(10)-helix, the Ac(5)c nonapeptide 6 formed a mixture of (P) 3(10)- and α-helices, and the Ac(5)c(dOM) nonapeptides 7 and 8 formed (P) α-helices. X-Ray crystallographic analysis revealed that the Aib hexapeptide 1 formed a (P) 3(10)-helix, while (S,S)-Ac(5)c(dOM) hexapeptide 3 formed a (P) α-helix. In addition, the Ac(5)c nonapeptide 6 and (R,R)-Ac(5)c(dOM) nonapeptide 8 formed (P) α-helices. The Aib and achiral Ac(5)c residues have the propensity to form 3(10)-helices in short peptides, whereas the chiral Ac(5)c(dOM) residues have a penchant for forming α-helices.     

Investigation of naphthyridines. 16. Synthesis of derivatives of 2,5-dioxo-1,2,5,6,7,8-hexahydro-1,6-naphthyridine-3-carboxylic acids from anilides (hydrazides) of 6-oxo-2-styrylnicotinic acids

Heating anilides (hydrazides) of 5-cyano-6-oxo-2-styrylnicotinic acids in polyphosphoric acid (PPA) leads to amides of 7-aryl-2,5-dioxo-6-phenyl(amino)-1,2,5,6,7,8-hexahydro-1,6-naphthyridine-3-carboxylic acids, which on heating with perchloric acid in acetic acid give the corresponding acids.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 12, pp. 1809–1812, December, 2004.For Part 15 see [1].