Self-Organization Ability of Chiral Nα-Substituted, Nß-Boc Protected α-Hydrazinoacetamides in the Crystal and Solution States.

The limitations of peptides have severely hampered their use in pharmacology, thus prompting the design of new peptidomimetic foldamers. This requires precise knowledge of the secondary structure of new compounds and the ability to predict their folding. Conformational studies of the basic units of these foldamers can be of invaluable assistance in designing new bioactive compounds. To this end, we investigated the conformation of three chiral Nα-substituted, Nß-Boc protected α-hydrazinoacetamide model compounds containing various side chains both on the Nα- and Cα-atoms in both the crystal and solution states. On the basis of IR absorption spectroscopy, NMR, molecular dynamics calculations and X-ray diffraction experiments, we demonstrated that these three models adopt conformational preferences, relying on eight-, six- or five-membered H-bonded pseudocycles (C8, C6 or C5), depending on the steric bulk of both Nα- or Cα-side chains. This study sheds light onto the versatile folding ability of the specific class of α-Nα-hydrazinopeptides and emphasizes the key role of the Cα-side chain on the conformational preference of the folding.

Spontaneous Self-Assembly of Fully Protected Ester 1:1 [α/α-Nα-Bn-hydrazino] Pseudodipeptides into a Twisted Parallel ß-Sheet in the Crystal State.

Previous studies have demonstrated that amidic α/ß-pseudodipeptides, 1:1 [α/α-Nα-Bn-hydrazino], have the ability to fold via a succession of γ-turn (C7 pseudocycle) and hydrazinoturn in CDCl3 solution, their amide terminals enabling the formation of an intramolecular H-bond network. Despite their lack of a primary amide terminals allowing the formation of the hydrazinoturn, their ester counterparts 1-4 were proven to self-assemble into C6 and C7 pseudocycles by intramolecular H-bonds in solution state and into an uncommon twisted parallel ß-sheet through intermolecular H-bonding in the crystal state to form a supramolecular helix, with eight molecules needed to complete a full 360° rotation. Such self-organization (with eight molecules) has only been observed in a specific α/α-pseudodipeptide, depsipeptide (Boc-Leu-Lac-OEt). Relying on IR absorption, NMR, X-ray diffraction, and CD analyses, the aim of this study was to demonstrate that stereoisomers of ester 1:1 [α/α-Nα-Bn-hydrazino] pseudodipeptides 1-4 are able to self-assemble into this ß-helical structure. The absolute configuration of the asymmetric Cα-atom of the α-amino acid residue influences the left- or right-handed twist without changing the pitch of the formed helix.

Evidence of nanotubular self-organization in solution and solid states of heterochiral cyclo 1:1 [α/α-N(α)-Bn-hydrazino]mers series.

The cyclization of heterochiral 1:1 [α/α-N(α)-Bn-hydrazino]mers leads to the corresponding cyclotetramer and cyclohexamer 3 and 4. X-ray crystallographic analysis of 3 unveils its ability to self-assemble into nanotubular structures. Further experiments conducted in the solid state through SEM analyses demonstrate the capability of 3 and 4 to form aerogels consisting of a network of nontwisted fibers, thus confirming the presence of self-organization within this series of mixed-hydrazinopeptides. Subsequent FTIR and NMR studies demonstrate the presence of an equilibrium between monomeric (intramolecular H-bonds) and nanotubular (intermolecular H-bonds) forms in solution. This equilibrium can be modified by varying the solvent.

A favorable, narrow, δ(h) Hansen-parameter domain for gelation of low-molecular-weight amino acid derivatives.

In recent years, the design of new low-molecular-weight gelators (LMWGs) has attracted considerable attention because of the interesting supramolecular architectures as well as industrial applications. In this context, the role of the organic solvent in determining the organogelation behavior is a central question. Herein we report the results of a systematic study of the organogelation behavior of amino acid derivatives in a wide range of solvents to establish a relationship between the nature of the solvent and the formation of the gel. We highlight that the majority of the gelified solvents are aromatic, except for carbon tetrachloride and tetrachloroethylene. In addition, different parameters related to the nature of the solvent were considered and their influence on the physical properties of gelation was evaluated. The hydrogen-bonding Hansen parameter (δ(h)) allows us to draw a narrow favorable δ(h) domain for gelation in the range of 0.2-1.4 (cal cm(-3))(1/2). Furthermore, a general increase of the Hildebrand parameter (δ) leads to the formation of poor gels (small gelation numbers, GNs) in aromatic solvents. Scanning electron microscopy (SEM) revealed that the gels prepared from (l)-phenylalanine and (l)-leucine derivatives in different solvents are composed of an entangled 3D fibrillar network, the diameter of which is only slightly influenced by the nature of the solvent.

Evidence of intercolumnar π-π stacking interactions in amino-acid-based low-molecular-weight organogels.

A comparative IR and NMR study of two low-molecular-weight organogels (LMWGs) based on aminoacid derivatives let us point out the hierarchy of the gelation assembly process. Different association states of corresponding organogelator molecules can be observed leading to the supramolecular organization of gel. A first hydrogen bond network of gelators leads to the formation of "head-to-tail" stacking-up, which can be assembled afterward one to the other by π-π stacking interactions. These small supramolecular aggregates (incipient precursor) are still visible in NMR spectra, and they represent, for example, 36% of the total amount of gelator in the case of the L-phenylalanine derivative (gelator 1) at 1 wt % in toluene. Finally, in the last step, the incipient precursor tends to form the expected 3D fibrillar network responsible for the gelation phenomenon. Temperature-dependent IR and NMR experiments allowed us to identify these different states clearly.

Cyclohexamer [-(d-Phe-azaPhe-Ala)2-]: good candidate to formulate supramolecular organogels.

Molecular self-assembly is a fascinating process which has become an area of great interest in supramolecular chemistry, as it leads in certain cases to molecular gels. Organogels formulated from low molecular weight compounds (LMWOGs) have attracted much interest in the past decades due to their applications as new soft materials. Herein, we report on the ability of the cyclic pseudopeptide cyclo-[-(d-Phe-azaPhe-Ala)2-] (2) to self-assemble in some aromatic solvents and to form organogels driven by non-covalent forces, mainly hydrogen bonding and π-stacking interactions. Comprehensive FTIR and NMR studies emphasized that this cyclic aza-peptide adopts a ß-turn conformation at low concentration in toluene, while an equilibrium between the monomeric states (intramolecular forces) and the supramolecular structures (intra- and intermolecular forces) is established at high concentration (gel state). Rheological investigations of the organogels highlight the dependence of their stiffness (up to ∼4 kPa) and sol/gel transition temperatures (up to 100 °C) as a function of the solvent and concentration of gelator used. The formulation of fibrous structures confirmed the phenomenon of self-assembly. Finally, we found that cyclo-[-(d-Phe-azaPhe-Ala)2-] is an effective organogelator for application in phase selective gelation (PSG) of organic solvents from aqueous/organic mixtures with recovery percents up to 96%.

Dimer disruption and monomer sequestration by alkyl tripeptides are successful strategies for inhibiting wild-type and multidrug-resistant mutated HIV-1 proteases.

Wild-type and drug-resistant mutated HIV-1 proteases are active as dimers. This work describes the inhibition of their dimerization by a new series of alkyl tripeptides that target the four-stranded antiparallel beta-sheet formed by the interdigitation of the N- and C-monomer ends of each monomer. Analytical ultracentrifugation was used to give experimental evidence of their mode of action that is disruption of the active homodimer with formation of inactive monomer-inhibitor complexes. The minimum length of the alkyl chain needed to inhibit dimerization was established. Sequence variations led to a most potent HIV-PR dimerization inhibitor: palmitoyl-Leu-Glu-Tyr (Kid = 0.3 nM). Insertion of d-amino acids at the first two positions of the peptide moiety increased the inhibitor resistance to proteolysis without abolishing the inhibitory effect. Molecular dynamics simulations of the inhibitor series complexed with wild-type and mutated HIV-PR monomers corroborated the kinetic data. They suggested that the lipopeptide peptide moiety replaces the middle strand in the highly conserved intermolecular four-stranded beta-sheet formed by the peptide termini of each monomer, and the alkyl chain is tightly grasped by the active site groove capped by the beta-hairpin flap in a "superclosed" conformation. These new inhibitors were equally active in vitro against both wild-type and drug-resistant multimutated proteases, and the model suggested that the mutations in the monomer did not interfere with the inhibitor.

Aza-beta3-cyclopeptides: a new way of controlling nitrogen chirality.

Sixteen and 24 membered aza-beta(3)-peptidic macrocycles containing a alpha-hydrazinoacid or a beta(3)-aminoacid were synthesized. The conformation of these pseudopeptides was determined by using NH chemical shift analysis, NH extinction, VT-NMR experiments, and X-ray diffraction. The study shows that a stable conformation is retained between 223 and 413 K. The latter is characterized by an uninterrupted internal H-bond network and a syndiotactic arrangement of the asymmetric centers. It means that the presence of the optically pure residue acts as a conformational lock to select a single enantiomer through the cyclization by controlling the absolute configuration of all the nitrogen atoms. To our knowledge, this represents the first example of a dynamic enantioselection process involving several centers prone to pyramidal inversion. These results give a new impulsion to the control of nitrogen chirality, which remained limited to small cycles for 60 years.

Boc-AzAla-Ala-OMe.

THE TITLE COMPOUND (SYSTEMATIC NAME: tert-butyl 3-{[1-(methoxy-carbon-yl)eth-yl]amino-carbon-yl}-3-methyl-carbazate), C(11)H(21)N(3)O(5), is a precursor for the study of a new class of foldamer based on aza/α-dipeptide oligomerization [Abbas et al. (2009 ▶). Tetra-hedron Lett.50, 4158-4160]. The asymmetric unit consists of one mol-ecule in an extended conformation which is stabilized by inter-molecular N-H⋯O and C-H⋯O hydrogen bonding.

Di-tert-butyl 2-benzoyl-hydrazine-1,1-dicarboxyl-ate.

The crystal structure of the title compound, C(17)H(24)N(2)O(5), was determined in the course of our studies on the preparation of two families of pseudopeptides, viz. hydrazino- and N-amino- peptides. The most significant inter-action in the crystal structure is a bifurcated inter-molecular N-H⋯O hydrogen bond.

Solvent dynamical behavior in an organogel phase as studied by NMR relaxation and diffusion experiments.

An organogelation process depends on the gelator-solvent pair. This study deals with the solvent dynamics once the gelation process is completed. The first approach used is relaxometry, i.e., the measurement of toluene proton longitudinal relaxation time T(1) as a function of the proton NMR resonance frequency (here in the 5 kHz to 400 MHz range). Pure toluene exhibits an unexpected T(1) variation, which has been identified as paramagnetic relaxation resulting from an interaction of toluene with dissolved oxygen. In the gel phase, this contribution is retrieved with, in addition, a strong decay at low frequencies assigned to toluene molecules within the gel fibers. Comparison of dispersion curves of pure toluene and toluene in the gel phase leads to an estimate of the proportion of toluene embedded within the organogel (found around 40%). The second approach is based on carbon-13 T(1) and nuclear Overhauser effect measurements, the combination of these two parameters providing direct information about the reorientation of C-H bonds. It appears clearly that reorientation of toluene is the same in pure liquid and in the gel phase. The only noticeable changes in carbon-13 longitudinal relaxation times are due to the so-called chemical shift anisotropy (csa) mechanism and reflect slight modifications of the toluene electronic distribution in the gel phase. NMR diffusion measurements by the pulse gradient spin-echo (PGSE) method allow us to determine the diffusion coefficient of toluene inside the organogel. It is roughly two-thirds of the one in pure toluene, thus indicating that self-diffusion is the only dynamical parameter to be slightly affected when the solvent is inside the gel structure. The whole set of experimental observations leads to the conclusion that, once the gel is formed, the solvent becomes essentially passive, although an important fraction is located within the gel structure.

Crystal structure of Mycobacterium tuberculosis catalase-peroxidase.

The Mycobacterium tuberculosis catalase-peroxidase is a multifunctional heme-dependent enzyme that activates the core anti-tuberculosis drug isoniazid. Numerous studies have been undertaken to elucidate the enzyme-dependent mechanism of isoniazid activation, and it is well documented that mutations that reduce activity or inactivate the catalase-peroxidase lead to increased levels of isoniazid resistance in M. tuberculosis. Interpretation of the catalytic activities and the effects of mutations upon the action of the enzyme to date have been limited due to the lack of a three-dimensional structure for this enzyme. In order to provide a more accurate model of the three-dimensional structure of the M. tuberculosis catalase-peroxidase, we have crystallized the enzyme and now report its crystal structure refined to 2.4-A resolution. The structure reveals new information about dimer assembly and provides information about the location of residues that may play a role in catalysis including candidates for protein-based radical formation. Modeling and computational studies suggest that the binding site for isoniazid is located near the delta-meso heme edge rather than in a surface loop structure as currently proposed. The availability of a crystal structure for the M. tuberculosis catalase-peroxidase also permits structural and functional effects of mutations implicated in causing elevated levels of isoniazid resistance in clinical isolates to be interpreted with improved confidence.

Enzyme-catalyzed mechanism of isoniazid activation in class I and class III peroxidases.

There is an urgent need to understand the mechanism of activation of the frontline anti-tuberculosis drug isoniazid by the Mycobacterium tuberculosis catalase-peroxidase. To address this, a combination of NMR spectroscopic, biochemical, and computational methods have been used to obtain a model of the frontline anti-tuberculosis drug isoniazid bound to the active site of the class III peroxidase, horseradish peroxidase C. This information has been used in combination with the new crystal structure of the M. tuberculosis catalase-peroxidase to predict the mode of INH binding across the class I heme peroxidase family. An enzyme-catalyzed mechanism for INH activation is proposed that brings together structural, functional, and spectroscopic data from a variety of sources. Collectively, the information not only provides a molecular basis for understanding INH activation by the M. tuberculosis catalase-peroxidase but also establishes a new conceptual framework for testing hypotheses regarding the enzyme-catalyzed turnover of this compound in a number of heme peroxidases.