Synthesis of 310-Helix-Inducing Constrained Analogues of l-Proline

Conformational Effects through Hydrogen Bonding in a Constrained γ-Peptide Template: From Intraresidue Seven-Membered Rings to a Gel-Forming Sheet Structure

A series of three short oligomers (di-, tri-, and tetramers) of cis-2-(aminomethyl)cyclobutane carboxylic acid, a γ-amino acid featuring a cyclobutane ring constraint, were prepared, and their conformational behavior was examined spectroscopically and by molecular modeling. In dilute solutions, these peptides showed a number of low-energy conformers, including ribbonlike structures pleated around a rarely observed series of intramolecular seven-membered hydrogen bonds. In more concentrated solutions, these interactions defer to an organized supramolecular assembly, leading to thermoreversible organogel formation notably for the tripeptide, which produced fibrillar xerogels. In the solid state, the dipeptide adopted a fully extended conformation featuring a one-dimensional network of intermolecularly H-bonded molecules stacked in an antiparallel sheet alignment. This work provides unique insight into the interplay between inter- and intramolecular H-bonded conformer topologies for the same peptide template.

The conjugates of ferrocene-1,1'-diamine and amino acids. A novel synthetic approach and conformational analysis

A novel synthetic approach toward a poorly explored bioorganometallic consisting of ferrocene-1,1'-diamine bearing structurally and chirally diverse amino acid sequences is reported. Until now, ferrocene-1,1'-diamine was suitable for accommodating only identical amino acid sequences at its N-termini, leading to the symmetrically disubstituted homochiral products stabilized through a 14-membered intramolecular hydrogen-bonded ring as is seen in antiparallel β-sheet peptides. The key step of the novel synthetic pathway is the transformation of Ac-Ala-NH-Fn-COOH (5) (Fn = 1,1'-ferrocenylene) to orthogonally protected Ac-Ala-NH-Fn-NHBoc (7). The spectroscopic analysis (IR, NMR, CD) of the novel compounds, corroborated with DFT studies, suggests the interesting feature of the ferrocene-1,1'-diamine scaffold. The same hydrogen-bonding pattern, i.e. a 14-membered hydrogen-bonded ring, was determined both in solution and in the solid state, thus making them promising, yet simple scaffolds capable of mimicking β-sheet peptides. In vitro screening of potential anticancer activity in Hep G2 human liver carcinoma cells and Hs 578 T human breast cancer cells revealed a cytotoxic pattern for novel compounds (150-500 μM) with significantly decreased cell proliferation.

Design, synthesis, conformational analysis and application of indolizidin-2-one dipeptide mimics

Growth in the field of peptide mimicry over the past few decades has resulted in the synthesis of many new compounds and the investigation of novel pharmacological agents. Azabicyclo[X.Y.0]alkanone amino acids are among the attractive classes of constrained mimics, because they can create rigid peptide structures for probing the conformation and roles of natural motifs in recognition events important for biological activity. Herein, we review the last ten years of the synthesis, conformational analysis and activity of analogs of the azabicyclo[4.3.0]alkan-2-one amino acid subclass, so-called indolizidin-2-one amino acids, with particular attention on their employment as inputs for biological applications.

Direct chromatographic enantioresolution of fully constrained β-amino acids: exploring the use of high-molecular weight chiral selectors

To the best of our knowledge enantioselective chromatographic protocols on β-amino acids with polysaccharide-based chiral stationary phases (CSPs) have not yet appeared in the literature. Therefore, the primary objective of this work was the development of chromatographic methods based on the use of an amylose derivative CSP (Lux Amylose-2), enabling the direct normal-phase (NP) enantioresolution of four fully constrained β-amino acids. Also, the results obtained with the glycopeptide-type Chirobiotic T column employed in the usual polar-ionic (PI) mode of elution are compared with those achieved with the polysaccharide-based phase. The Lux Amylose-2 column, in combination with alkyl sulfonic acid containing NP eluent systems, prevailed over the Chirobiotic T one, when used under the PI mode of elution, and hence can be considered as the elective choice for the enantioseparation of this class of rigid β-amino acids. Moreover, the extraordinarily high α (up to 4.60) and R S (up to 10.60) values provided by the polysaccharidic polymer, especially when used with camphor sulfonic acid containing eluent systems, make it also suitable for preparative-scale enantioisolations.

The practice of ring constraint in peptidomimetics using bicyclic and polycyclic amino acids

Medicinal chemistry has witnessed major advances with the discovery of small synthetic molecules that mimic natural peptidic substrates. These small synthetic mimics do not undergo proteolytic degradation, an advantage they hold over their natural counterparts. Small synthetic molecules make up a number of life-saving marketed drugs that inhibit certain physiologically relevant proteases. The advent of sophisticated instrumental methods, such as X-ray crystallography and high-field NMR, has played a pivotal role in the design of structure-based enzyme inhibitors. Highly stereocontrolled methods of synthesis have led to a variety of functionally diverse molecules that function as peptidomimetics because they have isosteric subunits not affected by proteolytic enzymes. Further studies to optimize biological activity and achieve desirable pharmacokinetic profiles can eventually lead to drug substances. The practice of constraining natural amino acids like their conformationally rigid counterparts has been highly successful in the design and synthesis of peptidomimetic molecules. With some notable exceptions, structural information gathered from protein X-ray crystallography of therapeutically relevant target enzymes, alone or in complex forms with inhibitor molecules, has been instrumental in the design of peptidomimetics. For example, a significant number have become marketed drugs as antihypertensives and antivirals. Natural products have also been a source of inspiration for the design and synthesis of truncated analogues with the intention of maintaining, or even improving, their biological activities. However, lower molecular weight peptides are not suitable as therapeutic agents because they are subject to rapid amide proteolysis. They are poorly transported to the brain and rapidly excreted through the liver and kidney. Thus, lower molecular weight peptides are eliminated as potential drug substances in clinical practice. A synthetic peptidomimetic is needed that is resistant to cleavage but maintains its biological activity. Conformationally constrained monocyclic and bicyclic unnatural amino acids can be directly incorporated in a potential inhibitor molecule as part of the design element. In this Account, we describe our efforts in the synthesis of constrained azacycles that contain proline or pipecolic acid as an integral part of bicyclic and polycyclic amino acids. We devised syntheses of conformationally biased monocyclic, bicyclic, and polycyclic amino acid analogues, into which pharmacologically or structurally relevant functional groups were incorporated. Stereocontrolled reactions for C-C, C-N, and C-O bond formation had to be implemented on appropriately protected amino acid frameworks. A number of these frameworks provided access to functionally diverse scaffolds for further use as core subunits in more elaborated structures. Specific applications as peptidomimetics of natural substrates for relevant enzymes, such as thrombin, were also pursued, resulting in highly active inhibitors in vitro.

Designed peptides with homochiral and heterochiral diproline templates as conformational constraints

Diproline segments have been advanced as templates for nucleation of folded structure in designed peptides. The conformational space available to homochiral and heterochiral diproline segments has been probed by crystallographic and NMR studies on model peptides containing L-Pro-L-Pro and D-Pro-L-Pro units. Four distinct classes of model peptides have been investigated: a) isolated D-Pro-L-Pro segments which form type II' beta-turn; b) D-Pro-L-Pro-L-Xxx sequences which form type II'-I (betaII'-I, consecutive beta-turns) turns; c) D-Pro-L-Pro-D-Xxx sequences; d) L-Pro-L-Pro-L-Xxx sequences. A total of 17 peptide crystal structures containing diproline segments are reported. Peptides of the type Piv-D-Pro-L-Pro-L-Xxx-NHMe are conformationally homogeneous, adopting consecutive beta-turn conformations. Peptides in the series Piv-D-Pro-L-Pro-D-Xxx-NHMe and Piv-L-Pro-L-Pro-L-Xxx-NHMe, display a heterogeneity of structures in crystals. A type VIa beta-turn conformation is characterized in Piv-L-Pro-L-Pro-L-Phe-OMe (18), while an example of a 5-->1 hydrogen bonded alpha-turn is observed in crystals of Piv-D-Pro-L-Pro-D-Ala-NHMe (11). An analysis of pyrrolidine conformations suggests a preferred proline puckering geometry is favored only in the case of heterochiral diproline segments. Solution NMR studies, reveal a strong conformational influence of the C-terminal Xxx residues on the structures of diproline segments. In L-Pro-L-Pro-L-Xxx sequences, the Xxx residues strongly determine the population of Pro-Pro cis conformers, with an overwhelming population of the trans form in L-Xxx=L-Ala (19).

Hybrid Peptide Design. Hydrogen Bonded Conformations in Peptides Containing the Stereochemically Constrained γ-Amino Acid Residue, Gabapentin

The crystal structure of 12 peptides containing the conformationally constrained 1-(aminomethyl)cyclohexaneacetic acid, gabapentin (Gpn), are reported. In all the 39 Gpn residues conformationally characterized so far, the torsion angles about the Calpha-Cbeta and Cbeta-Cgamma bonds are restricted to the gauche conformation (+/-60 degrees ). The Gpn residue is constrained to adopt folded conformations resulting in the formation of intramolecularly hydrogen-bonded structures even in short peptides. The peptides Boc-Ac6c-Gpn-OMe 1 and Boc-Gpn-Aib-Gpn-Aib-OMe 2 provide examples of C7 conformation; peptides Boc-Gpn-Aib-OH 3, Boc-Ac6c-Gpn-OH 4, Boc-Val-Pro-Gpn-OH 5, Piv-Pro-Gpn-Val-OMe 6, and Boc-Gpn-Gpn-Leu-OMe 7 provide examples of C9 conformation; peptide Boc-Ala-Aib-Gpn-Aib-Ala-OMe 8 provides an example of C12 conformation and peptides Boc-betaLeu-Gpn-Val-OMe 9 and Boc-betaPhe-Gpn-Phe-OMe 10 provide examples of C13 conformation. Gpn peptides provide examples of backbone expanded mimetics for canonical alpha-peptide turns like the gamma (C7) and the beta (C10) turns. The hybrid betagamma sequences provide an example of a mimetic of the C13 alpha-turn formed by three contiguous alpha-amino acid residues. Two examples of folded tripeptide structures, Boc-Gpn-betaPhe-Leu-OMe 11 and Boc-Aib-Gpn-betaPhg-NHMe 12, lacking internal hydrogen bonds are also presented. An analysis of available Gpn residue conformations provides the basis for future design of folded hybrid peptides.

Diproline Templates as Folding Nuclei in Designed Peptides. Conformational Analysis of Synthetic Peptide Helices Containing Amino Terminal Pro-Pro Segments

The effect of N-terminal diproline segments in nucleating helical folding in designed peptides has been studied in two model sequences Piv-Pro-Pro-Aib-Leu-Aib-Phe-OMe (1) and Boc-Aib-Pro-Pro-Aib-Val-Ala-Phe-OMe (2). The structure of 1 in crystals, determined by X-ray diffraction, reveals a helical (alphaR) conformation for the segment residues 2 to 5, stabilized by one 4-->1 hydrogen bond and two 5-->1 interactions. The N-terminus residue, Pro(1) adopts a polyproline II (P(II)) conformation. NMR studies in three different solvent systems support a conformation similar to that observed in crystals. In the apolar solvent CDCl3, NOE data favor the population of both completely helical and partially unfolded structures. In the former, the Pro-Pro segment adopts an alphaR-alphaR conformation, whereas in the latter, a P(II)-alphaR structure is established. The conformational equilibrium shifts in favor of the P(II)-alphaR structure in solvents like methanol and DMSO. A significant population of the Pro(1)-Pro(2) cis conformer is also observed. The NMR results are consistent with the population of at least three conformational states about Pro-Pro segment: trans alphaR-alphaR, trans P(II)-alphaR and cis P(II)-alphaR. Of these, the two trans conformers are in rapid dynamic exchange on the NMR time scale, whereas the interconversion between cis and trans form is slow. Similar results are obtained with peptide 2. Analysis of 462 diproline segments in protein crystal structures reveals 25 examples of the alphaR-alphaR conformation followed by a helix. Modeling and energy minimization studies suggest that both P(II)-alphaR and alphaR-alphaR conformations have very similar energies in the model hexapeptide 1.

Controlled synthesis of thermoresponsive polymers derived from l-proline via RAFT polymerization

Well-defined polymers derived from L-proline are synthesized using reversible addition-fragmentation chain transfer (RAFT) polymerization and the amino acid-based polymers exhibit thermosensitive phase separation at lower critical solution temperatures (LCST = 15-45 degrees C) in aqueous medium.

Bis(amino acid) derivatives of 1,4-diamino-2-butyne that adopt a C2-symmetric turn conformation

1,4-Diamino-2-butyne was prepared from 1,4-dichloro-2-butyne via 1,4-diazido-2-butyne. Bis(amino acid) derivatives of 1,4-diamino-2-butyne having the general structure (Boc-Xxx-NHCH2C[triple bond])2 (Xxx = Ala, Phe and Met) were prepared and examined by 1H NMR spectroscopy. Using chemical shift, coupling constant and DMSO titration data it is found that these compounds adopt a C2-symmetric turn conformation featuring two intramolecular hydrogen bonds.